Criteria For Delimitation Research Articles

A phylogenetic approach to delimitate species in a probabilistic way.

Different species concepts and their associated criteria have been used to delimit species boundaries, such as the absence of gene flow for the biological species concept and the presence of morphological distinction for the morphological species concept. The need for different delimitation criteria largely reflects the fact that species are generated under various speciation mechanisms. A key question is how to make species delimitation consistent in a species group, especially when we want to delimit the species boundaries over many newly discovered evolutionary lineages and add these new lineages into a comparative analysis. Instead of forcing a single definition of 'species', we can acknowledge different delimitation criteria by modelling how fast lineages in a species group evolve to meet these criteria along a phylogenetic tree. This study presents such a new model and a new delimitation approach that calculates the probability of each possible species identity of a lineage. We use simulations to show that our likelihood function gives accurate estimates of parameters in the model and our approach have high power to correctly identify species identities. We apply the approach to lineages in two real species groups that already have genomic and morphological evidence for their species identities. Our approach gives consistent inference of species identities with these existing pieces of evidence. We also demonstrate how to use our model to test a popular hypothesis about speciation process across all lineages in a species group and discuss further extension of the model to study speciation.

Complex species structure of Lecithaster salmonis (Digenea: Lecithasteridae), a fish parasite in the Arctic and Pacific Northwest.

Studying complexes of cryptic or pseudocryptic species opens new horizons for the understanding of speciation processes, an important yet vague issue for the digeneans. We investigated a hemiuroidean trematode Lecithaster salmonis across a wide geographic range including the northern European seas (White, Barents, and Pechora), East Siberian Sea, and the Pacific Northwest (Sea of Okhotsk and Sea of Japan). The goals were to explore the genetic diversity within L. salmonis through mitochondrial (cox1 and nad5 genes) and ribosomal (ITS1, ITS2, 28S rDNA) marker sequences, to study morphometry of maritae, and to revise the life cycle data. Mitochondrial markers showed that L. salmonis is likely divided into six lineages (referred to as operational taxonomic units, OTUs), which often occur in sympatry, sometimes in a single host specimen. Variation in rDNA was not consistent with that in the mitochondrial markers. Morphometric analysis of maritae was performed for four out of six OTUs; it showed that some OTUs had significant differences from the others, but some did not. The effect of host species on the morphometric characteristics cannot be excluded. Intramolluscan stages were identified for two OTUs; they differed clearly by the structure of cercariae and also by the species of the first intermediate host. The case of L. salmonis is instructive in how different criteria for species delimitation can contradict each other. We regard this as a sign of recent or ongoing speciation and suggest using the name Lecithaster cf. salmonis. The most promising criteria to differentiate genetic lineages within L. cf. salmonis are first intermediate hosts and morphological characteristics of the cercariae: shape of the delivery tube and caudal cyst, and length of the filamentous appendage.

A new family of ant-associated fungi in Chaetothyriales

The order Chaetothyriales comprises the black yeasts and relatives, of which numerous species are prevalent as opportunists on human hosts. The present paper introduces a clade of species that live in ant nests inside hollow structures of tropical plants (so-called domatia) and their closest relatives. To clarify the evolutionary trajectory of the domatia-associated clade, molecular, morphological, and physiological data were analysed. The position of the domatia clade within the Chaetothyriales was assessed by phylogenetic analysis of ITS and LSU. Species delimitations were calculated and genealogical concordance performed with a dataset including the gene of the ribosomal operon, β-tubulin (BT2) and RNA polymerase II largest subunit (RBP1). Genome sequencing allowed additional analysis of mating types, mitochondrial genomes, and estimation of a species tree based on the proteins of 770 single copy orthologous genes. A new family with two new genera in Chaetothyriales was introduced to accommodate the taxa from ant-inhabited domatia and a related clade of plant- and rock-colonizing species. The family is monophyletic and has strong statistical support. Although species delimitation criteria suggested the separation of more than 10 species in the domatia-clade, genealogical concordance of ribosomal and housekeeping gene markers indicated genetic exchange. Seven new species were delineated, with species also being characterized by phenotypic features of fungal colony morphology, micromorphology, physiology and ecology. However, intra-specific variability remained exceptionally large and did not always match with ecological and geographic data. It is hypothesized that the high degrees of intra- and interspecific variability of some of the clades acknowledged as separate species might be related to extended periods of molecular evolution. The newly described species seem to have their preferred habitat in tropical ant nests, and they have adapted to this specific environment. Ant-domatia provide a remarkable habitat rich in volatile chemicals, which could be tolerated by the fungi under study. The family is distantly related to the family Herpotrichiellaceae comprising numerous human-opportunistic species, where hydrocarbon tolerance has been hypothesized to play a role in black yeast evolution.

Integrity-centered framework for determining protected areas boundary: An application in the China's national park

National parks are critical components of protected areas and are drawing increased global attention. Clear and rational boundaries may provide a scientific foundation for the sustainable protection and management of these areas. However, criteria for feasible national park delimitation and techniques for resolving conflicts between socioeconomic development and environmental protection are still poorly defined, particularly regarding integrity during park establishment. Consequently, a systematic analytical framework is essential for advancing research and practice. This study developed a systematic framework to determine the spatial boundaries, using the Kunlun Mountain region in China as a case for empirical analysis. Key issues in national park development—ecology and management—were systematically integrated into this framework. Most importantly, spatial connectivity, a critical concern in national park planning, was thoroughly considered for improving integrity optimization, an aspect often overlooked in previous delimitation studies. The results demonstrated that our framework effectively identified potential national park boundaries, achieving a balance between development and conservation. Furthermore, core protected and general control areas were delineated to support differentiated management approaches. This framework offers a scientific foundation for policymakers and managers to pursue sustainable protection and management of national parks.

Taxonomy of Anthologies According to the Criteria of Delimitation

Anthologies have usually been approached in relation to the canon and have usually been criticised for their inclusions and omissions. Yet anthology criticism ought to firstly acknowledge that the selection process stems from a concrete understanding of literature, tradition and its categories–period, genre, theme. These categories applied to the field of anthology-making are referred to as the criteria of delimitation, which condition which texts are apt to be anthologised. For this reason, Menand’s definition of tradition and its categories is set forth alongside Hopkins’s classification of anthologies in order to preserve the latter’s precise divisions–comprehensive, period, and trade anthologies–, to revise its terminology–genre anthology instead of generic anthology–, to demarcate the categories of the criteria of delimitation–critical anthologies are left out because they belong to the realm of the selection process–, and to propose a new class–the denomination of group anthologies for those collections which focus on the representativity of social groups. Thus, the criteria of delimitation, derived from the categories of tradition, offer a possible taxonomy of anthologies: comprehensive, period, genre, trade and group anthologies.

The need for a strict delimitation of early tree life stages in vegetation ecology

AbstractAimFor practical and theoretical purposes, ecological studies commonly classify trees into five major life‐cycle stages: seed, seedling, sapling, juvenile and adult. Whereas the seed and adult stages are usually accurately delimited across studies, there are discrepancies and ambiguity in the categorization of seedlings, saplings and juveniles, which can significantly affect the conclusions of community ecology studies. Here we propose a standardized set of criteria intended for community‐level research for delimiting these three stages based on biological and ecological rationales.MethodsWe assessed the relevance of such standardization by conducting a meta‐analysis of the effects of two human‐caused disturbances (defaunation and logging) on each early tree life stage and examining differences in effect sizes and confidence intervals among: (1) studies that match our delimitation criteria, (2) studies that do not match these criteria, and (3) all studies grouped together regardless of the criteria they used.ResultsWe found stronger effects with narrower confidence intervals when considering only the studies that matched our standardized delimitation criteria. In fact, the proportion of significant effects was between 1.7 (defaunation) and 5.4 (logging) times higher in studies matching our delimitation criteria than in studies that do not match them, probably because confidence intervals were 2.3–3.1 times smaller in the former group than in the latter. For logging studies, the direction of the effects changed in 30%–50% of the cases when comparing the results from all data and studies not matching our criteria with the results of the studies matching our criteria, always from non‐significant to significant effects.ConclusionsThese findings underscore the need for an ecologically meaningful categorization of early tree life stages based on standardized measures to increase the confidence, accuracy, reproducibility and generalization in plant biology and community ecological research. Synthesis efforts will particularly benefit from this standardized protocol.

Subulicystidium perlongisporum (Trechisporales), the first record in Ukraine

In this article we report the first record of Subulicystidium perlongisporum, a noteworthy corticioid fungus, which has never been previously recorded in Ukraine. A detailed morphological description of the examined specimen, along with the original photos, ecological specifics and global distribution details of the species are provided. The criteria for delimitation of long-spored species of Subulicystidium are discussed.

Species and Speciation in the Termite-Cultivated Fungus Termitomyces

Termitomyces is a genus of basidiomycete fungi cultivated by termites of the subfamily Macrotermitinae. This symbiosis originated in central Africa, and subsequently, the fungus-growing termites have colonized almost the entire African continent including Madagascar as well as significant parts of Asia. Around 40 species of Termitomyces have been described based on morphology of the sexual fruit bodies, which are associated with some 330 species of fungus-growing termites distributed over 11 genera. However, the total number of fungal species may be higher as not all species regularly produce mushrooms, and morphological variation does not seem to be a reliable criterion for species delimitation in this group. In this study we estimated the total number of species based on ITS-barcode criteria and assessed host specificity and geographic differentiation to infer patterns of speciation. We estimated the total number of phylogenetic species using two methods of DNA sequence-based species delimitation; Automatic Barcode Gap Discovery (ABGD) and the Generalized Mixed Yule Coalescent (GMYC) model on a large dataset of over 1,500 ITS sequences from laboratory cultures, fungarium specimens and the public database NCBI Genbank. This resulted in an estimated 87 species hypotheses using ABGD and 94 species hypotheses using the GMYC model. A phylogenetic reconstruction was performed on representative sequences of the 87 species hypotheses identified by ABGD (the most conservative estimate) constrained by a well-supported phylogeny based on whole-genome data to address host specificity and geographical differentiation. Five main clades were recovered which generally were associated with species of one or two host genera, except for samples collected from the genera Microtermes and Ancistrotermes, which formed two separate non-sister clades. We did not find any evidence for long-term host fidelity as would be expected for species with strict uniparental vertical symbiont transmission. We found strict geographic separation between African and Asian species of Termitomyces and infer a minimum of seven inter-continental migrations. We show that epigeous fruiting of the T. microcarpus group has a single evolutionary origin in Africa and that fruiting in species of this group likely is induced by the fungus rather than by the host-termite species. In contrast, fruiting in the symbionts of some species of Microtermes and Macrotermes may be suppressed by the host-termite species, since mushrooms of certain fungal species are found when those species are associated with some termite-host genera, but never when associated with other host genera. We discuss some examples of incongruence between morphological and phylogenetic species concepts and give suggestions to improve the taxonomy of the genus Termitomyces.

Discovery of a novel spotted fever group Rickettsia, "Candidatus Rickettsia kedanie," in unfed larval chigger mites, Leptotrombidium scutellare.

Spotted fever group (SFG) rickettsia, the causative agent of SFG rickettsiosis, is predominantly carried by ticks, whereas Orientia tsutusgamushi, the causative agent of scrub typhus, is primarily transmitted by chigger mites in Japan. In this study, we attempted to isolate intracellular eubacteria from Leptotrombidium scutellare, a major vector of O. tsutsugamushi; moreover, we isolated an SFG rickettsia using a mosquito-derived cell line. Draft genome sequences of this unique isolate, by applying criteria for species delimitation, classified this isolate as a novel strain, proposed as "Rickettsia kedanie." Further genetic analysis identified conserved virulence factors, and the isolate successfully propagated in mammalian cells, suggesting its ability to cause diseases in humans. The presence of SFG rickettsia in unfed larvae implies potential dual-pathogen carriage and reflects a symbiotic relationship similar to that between the mites and O. tsutsugamushi, indicating possibility of its transovarial transmission from female adults. Furthermore, conserved genomic similarity of the novel isolate to known SFG rickettsia suggests potential multiple hosts, including chiggers and ticks. In the natural environment, ticks, chigger mites, and wild animals may carry new isolates, complicating the infection cycle and increasing the transmission risks to humans. This discovery challenges the conventional association of SFG rickettsia with ticks, emphasizing its implications for research and disease control. However, this study was confined to a particular species of chigger mites and geographic area, underscoring the necessity for additional studies to comprehend the ecological dynamics, host interactions, and health implications linked to this newly identified SFG rickettsia.

Next‐generation species delimitation and taxonomy: Implications for biogeography

AbstractAn accurate species‐level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population‐level lineages, the rise of integrative approaches to delimit such lineages, and the advent of high‐throughput sequencing have considerably renewed the discipline of taxonomy. Using genome‐scale molecular datasets, the extent of admixture across hybrid zones can now be effectively assessed and the evolutionary independence of lineages inferred, leading to more reliable and comparable species delimitation criteria. Substantially divergent but admixing phylogeographical lineages can conveniently be named as subspecies, thus avoiding taxonomic oversplitting and taxonomic inflation. At the same time, comprehensive DNA barcoding and DNA metabarcoding efforts are uncovering an enormous proportion of undiscovered biotic diversity, and we encourage the development of bioinformatic pipelines that combine high‐throughput species discovery and delimitation with diagnosis and scientific naming, to approach a biotic inventory of the globe without abandoning the established Linnaean system.

Assessing the role of taxonomic impediment in the knowledge on geographic distribution of Physidae (Gastropoda: Hygrophila) in South America, using an intensive-data approach.

There is a marked disparity in the state of knowledge of Holartic x Neotropical species of the freshwater snail family Physidae; the incipiency of data on Neotropical physids reflecting the lower number of dedicated specialists. The gaps in the knowledge on Neotropical physids have led to historical uncertainty about species validity. Revisiting the species is essential to reduce taxonomic impediment and delineating their probable distribution is the first step to attain this purpose. We aimed at critically analyze occurrence records of South American physids, compiled through an intensive search in the literature, biodiversity and molecular databases. We present a provisional characterization of the distribution of this family in South America, considering the probable versus the poorly documented distribution of the species. The critical underrepresentation of South American physids in collections, molecular databases and literature reinforces the role of taxonomic impediment in delaying the advance of the knowledge on species diversity. Malacological collections represented the main source of records, evidencing the relevance of unpublished data associated to specimens to assess distributional information on neglected groups. As most of the species are represented by shells, the reassessment of species identity and distribution must be done, using molecular and anatomical criteria for species delimitation.

Проблемы и подходы к выявлению границ агломераций Севера и Арктики России

Urban agglomerations are currently considered by both scientists and practitioners of public administration. However, the issue of identifying the actual boundaries and creating tools for the development of so-called “second” – and “third-tier” agglomerations, with cores in large and medium-sized cities, remains understudied. Nevertheless, such agglomerations can become development drivers for territories outside the settlement area, primarily in the North and the Arctic. The article aims to determine the composition and boundaries of northern and Arctic agglomerations of Russia considering their specificity. The study presents the authors’ methodological approach to the delimitation of agglomerations combining traditional (isochrones of transport accessibility, gravitational methods) and modern tools (GIS technologies, big data analytics of social networks). As a result, the composition and boundaries of three northern/Arctic agglomerations with cores in Arkhangelsk, Surgut, Norilsk were identified, their specific characteristics were highlighted: the actual borders often do not meet strict traditional criteria of delimitation, particularly, the 1.5-hour isochrone of transport accessibility of the core city due to the weakened effect of geographical proximity; according to the development criterion of the settlement system, two of them (Surgut, Arkhangelsk) can be attributed to agglomerations; despite the underdeveloped settlement framework (the development coefficient is less than 2.7) and a growing share of the core city population in the total population, satellite areas increasingly become economic centres of gravity of agglomerations. The study substantiated the expediency of applying a flexible approach to the delimitation of borders and selecting tools for the development of urban agglomerations, taking into account formation factors and their economic and geographical location, specifically in the North and non-North projections. Further research will involve an in-depth assessment of localisation and urbanisation effects of the studied agglomerations.

Species catalogue of Drymaeus (Mesembrinus) Alberts, 1850 (Gastropoda: Bulimulidae) from Brazil and new data on morphology and distribution of Drymaeus (Mesembrinus) interpunctus (Martens, 1887).

Herein, we attempted to obtain detailed data on the distribution of the species of Drymaeus (Mesembrinus) in Brazil, using biodiversity databases, malacological collections and literature as sources of occurrence records. We provided a catalogue of species, along with distribution maps. We also estimated the suitable distribution of Drymaeus (Mesembrinus) interpunctus using the maximum entropy approach. A detailed description of the anatomy of the soft parts of this species was provided, with new data on the pallial system. For each species we provided information on the compiled data associated with museum collections and the literature. Distribution maps including geographic boundaries, Brazilian biomes and altitude were made with QGIS software 3.16.10 Hannover. For niche modelling, nineteen bioclimatic variables and a topographic variable were used as predictors. The models were performed with MaxEnt version 3.3.3k. Most of the species are represented by scarce material in malacological collections; for some species, these records correspond to type material, indicating that they have not been recollected. Most of the species were represented by shells making anatomical comparison and DNA analysis difficult, limiting our ability to provide new criteria for species delimitation. Our results allowed us to expand the known distribution area for three species, Drymaeus dutaillyi, D. gereti and D. oreades, with new occurrence records in Brazil. The MaxEnt model showed a thin area of high suitability to D. (M.) interpunctus in the Southeastern Brazil, corresponding to the Atlantic Forest. Minimum temperature of the coldest month and mean temperature of coldest quarter were the variables that most influenced the development of the model. Drymaeus interpunctus was described based on specimens collected in Brazil without mention to the exact localities. Herein the new records from databases allowed to expand the known geographic distribution for this species and to infer its potential distribution. Although the type locality of D. interpunctus is in Brazil, the anatomy of the soft parts of specimens from this country was not previously described. The anatomy of the reproductive system of the specimens analyzed herein mostly corresponds to a previous description for specimens from Paraguay, except for the absence of penial sheath and the relative length of the bursa copulatrix duct. The results of niche modeling showed a thin area of high suitability for D. interpunctus and a vast area of moderate suitability, indicating that this species present a niche breadth that favors its occurrence in a range of different biomes, including less suitable areas. The small number of records obtained for most of the species and their restricted ranges associated with habitat destruction may indicate that they are of conservation concern.

The High-Low Arctic boundary: How is it determined and where is it located?

Geobotanical subdivision of landcover is a baseline for many studies. The High-Low Arctic boundary is considered to be of fundamental natural importance. The wide application of different delimitation schemes in various ecological studies and climatic scenarios raises the following questions: (i) What are the common criteria to define the High and Low Arctic? (ii) Could human impact significantly change the distribution of the delimitation criteria? (iii) Is the widely accepted temperature criterion still relevant given ongoing climate change? and (iv) Could we locate the High-Low Arctic boundary by mapping these criteria derived from modern open remote sensing and climatic data? Researchers rely on common criteria for geobotanical delimitation of the Arctic. Unified circumpolar criteria are based on the structure of vegetation cover and climate, while regional specifics are reflected in the floral composition. However, the published delimitation schemes vary greatly. The disagreement in the location of geobotanical boundaries across the studies manifests in poorly comparable results. While maintaining the common principles of geobotanical subdivision, we derived the boundary between the High and Low Arctic using the most up-to-date field data and modern techniques: species distribution modeling, radar, thermal and optical satellite imagery processing, and climatic data analysis. The position of the High-Low Arctic boundary in Western Siberia was clarified and mapped. The new boundary is located 50-100 km further north compared to all the previously presented ones. Long-term anthropogenic press contributes to a change in the vegetation structure but does not noticeably affect key species ranges. A previously specified climatic criterion for the High-Low Arctic boundary accepted in scientific literature has not coincided with the boundary in Western Siberia for over 70 years. The High-Low Arctic boundary is distinctly reflected in biodiversity distribution. The presented approach is appropriate for accurate mapping of the High-Low Arctic boundary in the circumpolar extent.

On the Relationship of the Residential Lease Agreement and the Hotel Services Agreement

There are a lot of difficulties with the qualification of contracts in law enforcement practice, which is explained by the complexity and the constant development of economic relations. One of the problems recently encountered by domestic courts relates to the distinction between the contract of rental accommodation and the contract of hotel services. At the moment there is no unity of the courts’ positions on the criteria of differentiation of these contracts, which requires a scientific assessment of this issue. The aim of the article was to form a theoretically grounded approach to the criteria of delimitation of the contract of lease of residential premises and the contract of hotel services. In order to achieve this aim we have set the following tasks: 1) to determine the features of the contract of tenancy and the contract for hotel services; 2) to explore the approaches existing in judicial practice; 3) to formulate criteria for distinguishing these contracts. The article was prepared with the use of general scientific methods (system, logical) and special legal methods (comparative-legal, formal-legal). The author comes to the conclusion that when differentiating a residential lease agreement and a hotel services contract, one should proceed from the presence or absence of a purpose of residence, which is characterized by a long-term legal relationship, the binding of a citizen to a given locality and independence in maintaining the premises in a condition suitable for living and meeting household needs.

Delimiting supervision zones to inform the revision of land reclamation management modes in coal mining areas: A perspective from the succession characteristics of rehabilitated vegetation

The rational delimitation of supervision zones is an important means of regional management that can effectively solve the problem of unbalanced development among reclaimed coal mine areas. In this study, 32 years of vegetation fractional coverage (VFC) series data from 1989 to 2020 were obtained for the area around the Pingshuo opencast coal mine. Then, the S-logistic function was applied to fit the VFC series data for each reclamation dump unit. Combined with the recognition results of coal mining and land reclamation years and by setting three delimitation criteria, the supervision zones of land reclamation that need to be better managed in the reclaimed dump sites were delimited. Finally, optimization revisions of the land reclamation management mode were proposed. The results showed that the effective reclamation zones of land reclamation occupied most of the study area, especially in the early reclaimed west dump, south dump and inner dump I areas of the Antaibao coal mine. The level one supervision zones, which were delineated as the general management zones, were mainly concentrated in the Anjialing inner dump, Nansigou dump, east dump, and west dump. The level two supervision zones, which were delineated as special management zones, were mainly concentrated in the Anjialing Nansigou dump site. Moreover, the Pingshuo coal mine dump sites were divided into four mode areas, namely, ecological conservation, ecological monitoring, ecological restoration, and ecological reconstruction, for the revision of land reclamation management. The proportion of area corresponding to each management mode was 49 %, 23 %, 24 % and 4 %, respectively. The management modes applicable to different reclaimed dump sites differed, and the specific management measures to be adopted depend on the succession pattern of the whole processes of rehabilitated vegetation. This study provides a new approach for delimitating the supervision zones of land reclamation and proposes revision management modes for the precise implementation of land reclamation development plans in coal mining areas.

A Reliable Criterion for the Correct Delimitation of the Foveal Avascular Zone in Diabetic Patients.

Manual segmentation of the Foveal Avascular Zone (FAZ) has a high level of variability. Research into retinas needs coherent segmentation sets with low variability. Retinal optical coherence tomography angiography (OCTA) images from type-1 diabetes mellitus (DM1), type-2 diabetes mellitus (DM2) and healthy patients were included. Superficial (SCP) and deep (DCP) capillary plexus FAZs were manually segmented by different observers. After comparing the results, a new criterion was established to reduce variability in the segmentations. The FAZ area and acircularity were also studied. The new segmentation criterion produces smaller areas (closer to the real FAZ) with lower variability than the different criteria of the explorers in both plexuses for the three groups. This was particularly noticeable for the DM2 group with damaged retinas. The acircularity values were also slightly reduced with the final criterion in all groups. The FAZ areas with lower values showed slightly higher acircularity values. We also have a consistent and coherent set of segmentations with which to continue our research. Manual segmentations of FAZ are generally carried out with little attention to the consistency of the measurements. A novel criterion for segmenting the FAZ allows segmentations made by different observers to be more similar.

A plea for preregistration in taxonomy

There are notoriously many different definitions of species and methods of species delimitation, forcing taxonomists to make a long range of methodological decisions in species delimitation. Because of this, there are sometimes multiple viable competing methodological paths, which could lead to different ranking (or even grouping) decisions. As a result, it is often unclear what it means for a group to be recognized as a species, the groups recognized as species are not always comparable, and some have even called ranking decisions ‘subjective’. To mitigate the problems this causes for users of taxonomy and taxonomists, we propose that taxonomists across the tree of life should start preregistering their research design and criteria for species delimitation in advance of their research. We argue that even if it were to require additional effort, preregistering taxonomic research would strongly benefit taxonomy in the long term, by increasing the transparency and usability of taxonomic outcomes and by reducing the need for ad hoc methodological decisions.

A unified view of homology.

As it spread through time and into distinct areas of science-from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology-the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of 'concepts of homology'; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 'concepts of homology' in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller's five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.

Were Neanderthals and Homo sapiens ‘good species’?

Prior to the advent of whole-genome sequencing in ancient humans, the likelihood that Homo sapiens and Neanderthals admixed has long been debated, mostly on the basis of phenotypic assessments alone. Today, evidence for archaic hominin admixture is being documented in an increasing number of studies, expanding the evidential basis of the debate on whether Homo sapiens and Neanderthals merit separate specific taxonomic status.Here we argue that while new evidence has provided us with a finer-grained picture of ancient intra- and intergroup demographic dynamics, it does not yet justify merging the Neanderthals in an expanded concept of Homo sapiens or abandoning specific taxonomies. We approach this issue and the apparent conflict between molecular and morphology-based taxonomies from a diachronic perspective on lineage divergence, highlighting how different taxonomic properties are expected to arise at different points in time, and from an integrative perspective on different species conceptions and delimitation criteria. We argue that in light of similar “invasions” of the genome among other animal taxa, full reproductive isolation as the final, litmus test for distinct species status should be rather considered a biologically misplaced expectation. Therefore, we suggest that specific nomenclature should not be perceived with embarrassment but rather be justifiably applied in human paleogenomic publications, maintaining congruence with zoological literature.We then briefly consider and problematize recent suggestions that human evolutionary diversification should now be best represented by a ‘braided stream” or a network. We conclude by putting our paleoanthropological case study in the broader context of species delimitation in the genomic era.