Definition Of Species Research Articles

An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane.

Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, FoF1-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.

Research on the social perception of invasive species: a systematic literature review

We conducted a systematic literature review of the current state of research on the social perceptions of invasive species, aiming to provide guidance towards transdisciplinary research and participatory decision making. In order to detect patterns regarding publication trends and factors determining social perceptions of invasive species, we applied qualitative content as well as quantitative data analysis. By applying content analysis, we identified five main categories of influence on the perception of invasive species: ecological conditions, social conditions, values and beliefs, impacts, and benefits. The disciplinary focus of the research was predominantly interdisciplinary, followed by a social sciences approach. Our review revealed a disproportionate use of quantitative methods in research on social perceptions of invasive species, yet quantitative methods were less likely to identify benefits as factors determining the perception of invasive species. However, without the understanding of perceived benefits, researchers and managers lack the socio-cultural context these species are embedded in. Our review also revealed the geographical, methodological and taxonomic bias of research on perceptions of invasive species. The majority of studies focused on the local public, whereas fewer than half of the studies focused on decision-makers. Furthermore, our results showed differences in the social perceptions of invasive species among different stakeholder groups. Consensus over the definition and terminology of invasive species was lacking whereas differences in terminology were clearly value-laden. In order to foster sustainable management of invasive species, research on social perceptions should focus on a transdisciplinary and transparent discourse about the inherent values of invasion science.

Who do growers trust? Engaging biosecurity knowledges to negotiate risk management in the north Queensland banana industry, Australia

A key issue for societal interaction with natural resources is to assess and manage incursions from pests and diseases. In this paper we focus on the biosecurity knowledge practices that are integral to the definition of invasive species and diseases, have impacts on the health of humans, natural and agricultural environments, and create policy problems for economy and society (Dixon, 2015). Rather than being an objective set of facts, theories and studies, biosecurity knowledge is a relational process. This process involves ongoing negotiations between diverse actors about what constitutes ‘good biosecurity’ (c.f. Hill, 2015). Negotiations are mediated between actors operating within different spheres of influence in their attempt to ‘make life safe’ (Higgins et al., 2016; Hinchcliffe et al., 2008; Hinchcliffe and Lavau, 2013). Multiple and sometimes contradictory biosecurity knowledges can be traced in different management narratives. These narratives, which are based on differing perceptions of ‘danger’, ‘threat’, ‘risk’ and ‘disease’ (Collier et al., 2004), influence biosecurity implementation programs (e.g. Robinson, 2017).

Middle Miocene Cephalotaxus (Taxaceae) from Yunnan, Southwest China, and its implications to taxonomy and evolution of the genus

The infrageneric taxonomy of the genus Cephalotaxus Siebold et Zuccarini ex Endlicher (Taxaceae) is controversial as morphological characters have been doubted to change coherently among species. Although the epidermal features are considered as important characters in the taxonomy of conifers, they have not been systematically studied in this genus. Neogene foliage shoots with well-preserved epidermal structure not only can provide systematic links to the extant species, but also have implications for the taxonomical definition of the extant species by their epidermal features. In this paper, the morphologies of leafy shoots combining epidermal structure of a Neogene Cephalotaxus, which was collected from the middle Miocene of Southwest China, and ten extant species (variants) were studied. Morphology as well as epidermal structures was compared among species (variants) in Cephalotaxus. Based on the comparisons, the taxonomical definition of extant species in genus Cephalotaxus are discussed. Our results indicate that leaf morphological characters in combination with the features of epidermal structure can distinguish species in genus Cephalotaxus. The fossil foliage shoots from the middle Miocene of Southwest China were assigned to a new species, C. maguanensis n. sp., which shows close affinities to the extant C. hainanensis. On the basis of leaf and epidermal information, we suggest there are seven extant species in Cephalotaxus. With global cooling and the uplift of the Qinghai-Tibet Plateau since the middle Miocene, the cooling climate induced the differentiation and southward expansions of C. maguanensis, and its extant offspring, C. hainanensis, is distributed to Hainan Island and the Indo-Chinese peninsula.

Mating Markets: A Naturally Selected Sex Allocation Theory of Sexual Selection

This article utilizes three premises. (1) There are commonly ecologically oriented, naturally selected specialized differences in frequency and/or quality as well as sexually selected differences between the sexes. (2) Sex in the sense of coming together and going apart (syngamy and meiosis in haploids) or going apart and coming together (meiosis and syngamy in diploids) is trade in these naturally selected differences, i.e., there is a mating market in sexual species. (3) While such trade is beneficial to the population as a whole, sexual competition and selection is conflict over the profits of that trade and can be detrimental to the population as a whole. These premises yield a naturally selected sex allocation theory of the possible directions and forms of sexual selection, i.e., one that includes costs as well as frequencies. This can explain conventional sex roles, the sex-role reversed, inter- as well as intrasexual selection, and passive as well as active choice. Any of these alternatives may be over mates, over gametes, or both. A hypothetical example based on density dependence relative to resources is provided, one that suggests that centrioles may be a cytoplasmic resource in males in multicellular animals, and which are the target of active choice and the mechanism of manipulation in passive female choice. As a whole, the approach yields a truly general theory of sexual selection, provides an alternative to the mechanism for Fisher’s principle, and gives a theoretical explanation for Mayr’s biological species definition.

Identification of the Mycobacterial Strains Isolated From Clinical Specimens Using hsp65 PCR-RFLP Method.

Objectives:It is important to identify mycobacteria at the species level, to distinguish pathogen from non-pathogenic species, to choose the appropriate treatment regimen and to collect epidemiological data. For the identification of mycobacteria, which are time-consuming and laborious with traditional methods, faster, more sensitive and reliable methods are needed. This study aims to investigate the suitability of the hsp65 Polymerase chain reaction-restriction fragment polymorphism (PCR-RFLP) method for routine laboratory use.Methods:In this study, 141 mycobacterial isolates were obtained from 1632 samples, which were sent to the Medical Microbiology Laboratory.Results:In the culture, mycobacteria were identified as 138 M. tuberculosis complex (MTBC) and three non-tuberculosis mycobacteria (NTM) by conventional methods. Using the hsp65 PCR-RFLP method, 137 isolates were identified as MTBC, four isolates as NTM. An isolate that was evaluated as MTBC because it was PNB sensitive by the conventional method was determined as NTM with the hsp65 method. In the identification of non-tuberculosis mycobacteria with the hsp65 PCR-RFLP method, one isolate was identified as M. abcessus and three isolates were identified as M. avium complex.Conclusion:In our study, it was concluded that the hsp65 PCR-RFLP method, which allows identification of mycobacteria, including NTMs, is a method that is cheap, easy and suitable for routine use to provide rapid information to the clinic. The scope of the agar and database used in the method is effective in the definition of the correct species.

Powstanie człowieka – niektóre kontrowersje

Niniejszy artykuł przedstawia niektóre kontrowersje dotyczące powstania człowieka. Pierwsza część podejmuje kwestię ustalenia pierwszego reprezentanta rodzaju ludzkiego. Dalsza część poświęcona jest zagadnieniu ewolucji Homo erectus prowadzącej do wyłonienia się Homo sapiens. Przedstawione są dwie, najbardziej skrajne pod względem swoich założeń teorie: hipoteza ewolucji wieloregionalnej oraz hipoteza afrykańskiego zastąpienia. W następnej kolejności omówione są różne definicje gatunku, stosowane przez przyrodników, opisana jest ich rola w procesie tworzenia taksonomii oraz interpretacji materiałów kostnych. Ostatnia część poświęcona jest kontrowersjom wokół neandertalczyka i jego roli w procesie ukształtowania się człowieka współczesnego.

Effectiveness of DNA Barcoding in Speyeria Butterflies at Small Geographic Scales

North American Speyeria butterflies are a group of conservation concern and a challenge to butterfly systematists. Establishing species delimitation and evolutionary relationships among Speyeria has proven difficult due to the polytypic nature of many species, coupled with the similarity of wing patterns of sympatric species. Recent molecular work has found not all Speyeria species to be monophyletic, which could be explained by improper species definitions, incomplete lineage sorting, or ongoing hybridization and introgression. However, these studies involved broad geographic sampling where molecular markers such as the DNA barcode may be especially subject to incomplete lineage sorting. Here we focus on a more local scale, analyzing the mitochondrial gene cytochrome oxidase subunit I (CoI) to test whether this marker recovers four sympatric Speyeria species: adiaste (W. H. Edwards, 1864), callippe (Boisduval, 1852), coronis (Behr, 1864), and zerene (Boisduval, 1852), in the greater San Francisco Bay Area. We found that CoI works well to separate all four species. Subspecies were less well-defined, with the S. adiaste subspecies clustering separately, but more mixed for the S. zerene and S. callippe subspecies. Overall, our analyses illustrate the utility of the DNA barcode for separating the Speyeria species and suggest further studies to investigate different geographic scales in order to elucidate genetic diversity patterns in this genus in North America.

Antifungal Susceptibility of Candida Species Isolated from Urine from Patients in a Neurosciences Intensive Care Unit

Background and Objectives: The incidence of fungal infections in immunocompromised patients, especially by Candida species, has increased in recent years. This study was designed to identify Candida species and determine antifungal susceptibility patterns isolated strains from urine samples of intensive care unit (ICU) patients. Materials and Methods: All the urine samples of neuroscience ICU patients were cultured on Blood agar, Cystine–Lactose–Electrolyte-deficient agar, and Sabouraud Dextrose Agar. The grown colony was identified with color pigmentation on Candida Differential Agar. The antifungal susceptibilities of all Candida species were carried out with fluconazole, amphotericin B, ketoconazole, itraconazole, clotrimazole, nystatin, and miconazole. The generated results were analyzed with SPSS software (Version 20, IBM Corp., Armonk, NY, USA). Results: Candida Species were found in both genders of ICU patients with respect to all age groups. Among 100 urinary tract infection patients, 14 individuals were affected with diabetes and cerebrovascular accident. Whereas other disease comorbidity renal tubular acidosis, subarachnoid hemorrhage, head injury, acute respiratory distress syndrome, hypertension, and others were 9, 8, 8, 5, 11, and 31, respectively. Candida albicans (38.09%) was the most frequently isolated species, followed by Candida glabrata (23.8%), Candida krusei (23.8%), and Candida tropicalis (2.85%). Resistance varies depending on the species and the respective antifungal agents. From among 7 antifungal agents, itraconazole showed highest percentage of sensitivity (81.8%). Conclusions: Species definition and determination of antifungal susceptibility patterns are advised for the proper management and treatment of patients at risk for systemic candidiasis. Resistance to antifungal agents is an alarming sign for the emerging common nosocomial fungal infections.

Four new choanoflagellate species from extreme saline environments: Indication for isolation-driven speciation exemplified by highly adapted Craspedida from salt flats in the Atacama Desert (Northern Chile)

With this study we aim to extend the knowledge on the biogeography of craspedid choanoflagellates with additional data from extreme environments. Up to now, very little is known about choanoflagellates from extreme saline environments, as most studies have focused on marine and freshwater habitats. Though previously investigated high saline ice biota communities have indicated a possible adaptation to environments with high salt concentrations. Hypersaline endorheic basins, so-called salt flats or salares from the Atacama Desert in Northern Chile provide an intense environment regarding fluctuating and extreme salinities, which allow for studies on evolutionary adaptations of protists to hypersaline conditions. This study focused on choanoflagellate species isolated from different salt flats, their morphological characteristics using light and electron microscopy, molecular marker genes (SSU and LSU rDNA) and their salinity tolerance. Here, we described four new craspedid choanoflagellate species, highly adapted to the hypersaline environment of the Atacama Desert. This study extends our knowledge on choanoflagellate phylogeny and ecology and can become the basis for further molecular studies to understand the mechanisms of adaptations. Additionally, we emphasize the need of adding additional data such as autecological characteristics to amend species definitions, which is only possible from cultivated strains. This data would support the use of molecular data originating from metagenomic analyses also in an ecological context.

Two new bioluminescent Henlea from Siberia and lack of molecular support for Hepatogaster (Annelida, Clitellata, Enchytraeidae)

Two bioluminescent enchytraeids, Henlea petushkovi sp. n. and Henlea rodionovae sp. n., are described from the Krasnoyarsk and Irkutsk regions in Eastern Siberia. These large potworms exhibit the typical light-production pattern reported repeatedly in the genus and recently elucidated by Russian researchers in its main biophysical and biochemical aspects. Morphology and DNA indicate that the two species are very closely related, but clearly divergent in the strength of the body wall (thick and opaque in H. petushkovi), structure of the prostomium (in H. rodionovae unprecedentedly wrinkled and mobile), brain shape (almost equilateral in H. petushkovi), size of coelomocytes (60–85 μm in H. petushkovi) and structure of intestinal diverticula (tulip-shaped in H. petushkovi, apple-shaped in H. rodionovae). Limited hybridization seems to occur between them, supported by a single case of conflict between COI and morphology, and a few intermediate morphotypes were noted in greenhouse populations. The new species are phylogenetically distant from all known congeners so far DNA-barcoded, even those that, like them, respond to the diagnosis of the putative subgenus Hepatogaster Cejka, 1910 (multitubular gut diverticula in VIII, indented brain, dorsal blood vessel from IX, prominent spermathecal glands, and nephridia from 5/6). In fact, our phylogenetic analyses dismiss Hepatogaster as an artificial (polyphyletic) taxon. Issues related to the definition of H. nasuta (Eisen, 1878), H. ochracea (Eisen, 1878) and H. irkutensis Burov, 1929, three species originally described from Siberia, indicate that Henlea taxonomy is still in a state of flux, as regards not only species interrelationships but also species definitions.

Evolution of plesiadapid mammals (Eutheria, Euarchonta, Plesiadapiformes) in Europe across the Paleocene/Eocene boundary: implications for phylogeny, biochronology and scenarios of dispersal

Plesiadapid mammals (Eutheria, Euarchonta, Plesiadapiformes) are well represented in the late Paleocene to early Eocene of Europe (reference levels MP6, MP7 and MP8+9), but relationships among the described species and their links to North American plesiadapids remain disputed. To better understand the evolution of the group in Europe, to explore its potential for biochronological dating and to test hypotheses on plesiadapid phylogenies and dispersal patterns between Europe and North America, a morphometric analysis was performed for a succession of plesiadapid assemblages bracketing the Paleocene/Eocene boundary (PEB) in the Paris Basin, including recently made collections from Montchenot (MP6) and Le Quesnoy (MP7). Both dental size and shape were analysed for nearly all positions of the permanent plesiadapid dentition. Size variation at Cernay (MP6) is consistent with the presence of at least two species of Plesiadapis. A morphological succession is found in European large-sized Plesiadapis, continuing beyond the PEB but showing no clear continuity with Eocene Platychoerops. Large-sized Plesiadapis from Berru (MP6) is distinctly different from P. tricuspidens, justifying the definition of a new species, P. berruensis. Species of Plesiadapis confirm the temporal succession of the localities Cernay, Berru, Le Quesnoy and Meudon, allowing definition of a refined biochronology in the Paris Basin, with Montchenot correlated approximately to Cernay. Comparisons between plesiadapids from Europe and North America indicate a separation from at least the terminal Tiffanian, suggesting correlation of the European reference level MP6 with the North American biozones Ti-5b and Ti-6. Convergent evolution in those lineages and in Platychoerops seems to be linked mainly to trends towards folivory.

Morphometric analysis of Middle Permian Eopolydiexodina and Monodiexodina species from the Dalan Formation, Zard‐Kuh Mountains, Zagros, Iran: An integration of traditional approach and quantitative analyses to identify fusulinid species

Eopolydiexodina and Monodiexodina individuals from the Middle Permian lower Dalan Member of the Dalan Formation in the Zard‐Kuh Mountains, southwest Iran, are quantitatively studied using histograms, normal probability plots, test of normality, and parametric (PCA and PCoA) and non‐parametric (NMDS) ordination techniques, in order to determine the accuracy of previously identified Eopolydiexodina and Monodiexodina species based on traditionally defined fusulinid parameters. Specimens of the genus Eopolydiexodina recorded in the lower Dalan Member have been previously assigned to one species and those of Monodiexodina are subdivided into one species and one subspecies. In the present study, 35 specimens from an Eopolydiexodina‐bearing bed in unit 11 and 40 individuals from a Monodiexodina‐bearing bed in unit 17 of the lower Dalan Member are selected. Observations of the histograms, normal probability plots, and test of normality for all the measured variables reveal that Eopolydiexodina and Monodiexodina individuals follow generally a normal distribution. The results of the principal component analysis (PCA), principle coordinate analysis (PCoA), and non‐metric multidimensional scaling (NMDS) suggest that the distribution of the studied individuals cannot be divided into different groups and only one species for Eopolydiexodina (E. aff. persica) and one species for Monodiexodina (M. aff. kattaensis) are identifiable. This study provides an example to show how the identification and definition of fusulinid species can be well constrained using both the traditional description approach and modern morphometric techniques together.

Characterization of indicator tree species in neotropical environments and implications for geological mapping

Geobotanical remote sensing (GbRS) in the strict sense is an indirect approach to obtain geological information in heavily vegetated areas for mineral prospecting and geological mapping. Using ultra- and hyperspectral technologies, the goals of this research comprise the definition and mapping of Neotropical tree species that are associated with geological facies (here called geo-environments) as well as their spectral discrimination at leaf and crown scales. This work also aims to investigate the possible relationship between leaf and crown spectral and chemical properties. The study was developed at the Mogi-Guaçu Ecological Station, in the Cerrado domain, southeastern Brazil. Data from 70 sample units, such as sediment texture and species from inventories, were first analyzed through vectorial quantization using Self-Organizing Maps (SOM). Principal Component Analysis and Spearman's ranked correlation coefficients were used to define geo-environments and target-species, respectively. Biochemical and visible to shortwave infrared (VSWIR) point spectral data (350–2500 nm) were collected from the leaves of the target-species, during both rainy and dry seasons. Spectral data from target-species crowns were obtained from hyperspectral images (530–2.532 nm, ProSpecTIR-VS sensor) with 1 m spatial resolution, and acquired in the beginning of the dry season. These spectra were classified using Multiple Endmember Spectral Mixture Analysis (MESMA) with two endmembers (EMs). Based on the MESMA results with two EMs, the best dataset per target-species was chosen for pixel-based image unmixing with three EMs (target-species, other vegetation types and shade). From 121 species sampled in the field, two proved to be associated with floodplains (Alluvial Deposits sequence), two with hills and plateaus of the Aquidauna Formation (Carboniferous sedimentary rocks, Paraná Basin), and two more with a specific facies of the Aquidauna Formation that has a distinctive presence of coarse and very coarse sand. Five target-species were well discriminated at the leaf scale, reaching 90.0% and 85.0% of global accuracies in the rainy season and in the dry season, respectively. Accurate spectral discrimination appears to be linked to the considerable biochemical variability of their leaves in both seasons. Three species were discriminated at the crown scale, with 70.6% of global accuracy. When eight other landscape scale vegetation classes were included in the analyses, only Qualea grandiflora Mart. produced a satisfactory accuracy (61.1% and 100% of producer and user's accuracies, respectively). The spatial distribution of its fraction in the unmixed image, particularly, matches with the geological facies to which it was associated in the field. Ecological requirements for successfully mapping indicator species include broad and random distribution of the target-species' population, and singular physiological, phenological (and spectral) behavior at the imagery acquisition date. Our study shows that, even in tropical conditions, it is possible to use plant species mapping to support geological delineation, where rock exposures are typically rare.

Evaluation of the interspecific competition within Agrobacterium spp. in the soil and rhizosphere of tomato and maize

Agrobacterium biovar 1 is responsible for crown gall disease of many plant species. However, according to the current species definition, this taxon displays too large a genomic divergence to be a single species. This is why it is considered as a complex of distinct genomic species. Members of this taxon are common inhabitants of soils and rhizospheres, with several species and strains commonly found in the same samples. Understanding factors that shape their populations is very important for ecological and epidemiological issues. In this regard, this study was aimed at assessing whether plant genotypes differentially select agrobacteria genomospecies in their root systems. To test this hypothesis, we followed the evolution of tagged Agrobacterium fabrum C58 strains co-inoculated with members of different genomospecies (G1, G4, G7 and G8), in the soil and the rhizosphere of tomato and maize seedling plants under controlled conditions. The total number of the agrobacterial population was always statistically higher in rhizospheres than in bulk soils, confirming that agrobacteria are rhizospheric bacteria. The plasmid, pTi, was found not to be necessary for either rhizosphere colonization or the multiplication of the C58 strain. The difference between proportions of co-introduced bacteria from different genomic species shows the presence of a competition between them, which can vary with the plant species. While there were no significant differences between the proportion of co-inoculated strains of G8 (J07 and C58Gmr) in either plant species, they were more abundant in tomato than maize rhizosphere.

Host specificity of parasitoids (Encyrtidae) toward armored scale insects (Diaspididae): Untangling the effect of cryptic species on quantitative food webs.

Host specificity of parasitoids may be measured by various specialization indices to assess the variation of interaction strength among species and the structure of the wider interaction network. However, the conclusions from analyses at the species and network levels may differ, which remains poorly explored. In addition, the recovery of cryptic species of hosts and parasitoids with molecular data may affect the structure of inferred interaction links. We quantified host specificity of hymenopteran parasitoids (family Encyrtidae) on armored scale insects (Hemiptera: Diaspididae) from a wide geographic sampling range across the Chinese Mainland based on both morphological and molecular species delimitation. Mitochondrial COI and nuclear 28S markers detected high cryptic species diversity in the encyrtids and to a lesser degree in the diaspidids, which divided generalist morphospecies into complexes of specialists and generalists. One‐to‐one reciprocal host–parasite links were increased in the molecular data set, but different quantitative species‐level indices produced contrasting estimates of specificity from various one‐to‐multiple and multiple‐to‐multiple host–parasite links. Network indices calculated from DNA‐based species, compared to morphology‐based species definitions, showed lower connectance and generality, but greater specialization and compartmentalization of the interaction network. We conclude that a high degree of cryptic species in host–parasitoid systems refines the true network structure and may cause us overestimating the stability of these interaction webs.

Biological compatibility between two temperate lineages of brown dog ticks, Rhipicephalus sanguineus (sensu lato)

BackgroundThe brown dog tick Rhipicephalus sanguineus (sensu stricto) is reputed to be the most widespread tick of domestic dogs worldwide and has also been implicated in the transmission of many pathogens to dogs and humans. For more than two centuries, Rh. sanguineus (s.s.) was regarded as a single taxon, even considering its poor original description and the inexistence of a type specimen. However, genetic and crossbreeding experiments have indicated the existence of at least two distinct taxa within this name: the so-called “temperate” and “tropical” lineages of Rh. sanguineus (sensu lato). Recent genetic studies have also demonstrated the existence of additional lineages of Rh. sanguineus (s.l.) in Europe and Asia. Herein, we assessed the biological compatibility between two lineages of Rh. sanguineus (s.l.) found in southern Europe, namely Rhipicephalus sp. I (from Italy) and Rhipicephalus sp. II (from Portugal).MethodsTicks morphologically identified as Rh. sanguineus (s.l.) were collected in southern Portugal and southern Italy. Tick colonies were established and crossbreeding experiments conducted. Morphological, biological and genetic analyses were conducted.ResultsCrossbreeding experiments confirmed that ticks from the two studied lineages were able to mate and generate fertile hybrids. Hybrid adult ticks always presented the same genotype of the mother, confirming maternal inheritance of mtDNA. However, larvae and nymphs originated from Rhipicephalus sp. I females presented mtDNA genotype of either Rhipicephalus sp. I or Rhipicephalus sp. II, suggesting the occurrence of paternal inheritance or mitochondrial heteroplasmy. While biologically compatible, these lineages are distinct genetically and phenotypically.ConclusionsThe temperate lineages of Rh. sanguineus (s.l.) studied herein are biologically compatible and genetic data obtained from both pure and hybrid lines indicate the occurrence of paternal inheritance or mitochondrial heteroplasmy. This study opens new research avenues and raises question regarding the usefulness of genetic data and crossbreeding experiments as criteria for the definition of cryptic species in ticks.

Which Taxa Are Alien? Criteria, Applications, and Uncertainties

Human activities such as the transport of species to new regions and modifications of the environment are increasingly reshaping the distribution of biota. Accordingly, developing robust, repeatable, and consistent definitions of alien species that serve scientific and policy purposes has become of prime importance. We provide a set of classification criteria that are widely applicable across taxa and realms and offer guidance on their use in practice. The criteria focus on (a) acknowledging the role of assessment uncertainty, (b) incorporating time since introduction, (c) considering infraspecific taxonomic ranks, and (d) differentiating between alien species whose survival depends on explicit human assistance from those that survive without such assistance. Furthermore, we make recommendations for reducing assessment uncertainty, suggest thresholds for species assessment, and develop an assessment scheme. We illustrate the application of the assessment criteria with case studies. Finally, the implications for alien species management, policy, and research are discussed.

Biological species in the viral world

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

ConSpeciFix: classifying prokaryotic species based on gene flow.

Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML.