Species Concept Research Articles

The diversity of animals identified as keystone species.

Although the keystone species concept was conceived of over 50 years ago, contemporary efforts to synthesize related literature have been limited. Our objective was to create a list of keystone animal species identified in the literature and to examine the variation in the traits of species and the ecosystem influences they elicit. We documented 230 species considered keystones. A clustering analysis classified them into five archetypes based on combinations of their taxonomic class, body size, trophic level, and role (consumers, modifiers, or prey). Although conservation and public perception of keystones primarily focuses on large vertebrate consumers, our analysis reveals that researchers have defined a wide diversity of keystone species, with large variation in associated ecosystem processes. Future research may confront ambiguity in the definition of keystone status, as well as clarify the type, abundance, and quality of data required to assign the term. Identifying keystones with increased rigor would not only enrich the literature but also inform intervention to safeguard threatened keystones and their associated influences on ecosystems.

Is the behaviour a feature that implies evolutionary consequences in the speciation?

In birds, similar behaviour decreases in dramatic form the distances among sister lineages. The current classification of the Chilean representatives of the passerine family Rhinocryptidae includes eight species. Moreover, differences between the two lineages of Chilean species of Scytalopus genera, and two subspecies of Scelorchilus. Scelorchilus albicollis albicollis vs. S. a. atacamae; S. rubecula rubecula vs. S.r. mochae, two species of Pteroptochos: P. castaneus and P. tarnii, and two subspecies: P.megapodius megapodius and P.m. atacamae are very scarce. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. Our results show how when integrating behaviour and ecological terms as biological traits next to morphological characters of the plumage, allows us to conclude that there is a decrease in the distances among sister lineages in the cluster tree.

Taxonomic disagreement about ranks in gray-area taxa: A vignette study

Abstract When producing species classifications, taxonomists are often confronted with gray-area cases. For example, because of incipient or shallow divergence, it can be scientifically valid both to split groups of organisms into separate species and to lump them together into one species. It has been claimed that, in such cases, the ranking decision is, in part, subjective and may differ between taxonomists because of differences in their conceptions of species or even in conservation values. In the present article, we use a vignette study to empirically test this claim and to explore the drivers of taxonomic decision-making in gray-area cases. For three fictional taxonomic scenarios, we asked the opinion of a sample of taxonomists on one of slightly different versions of an abstract containing a decision on species status. The cases were explicitly designed to represent gray-area cases, and the differences between versions related to potential drivers of decisions, such as information on conservation status, different kinds of additional evidence, and information on the presence or absence of gene flow. In general, our results suggest that taxonomists tend to disagree at least moderately about species-ranking decisions in gray-area cases even when they are presented with the same data. We did not find evidence that species concepts or conservation values are strong drivers of taxonomic disagreement. Instead, operational concerns, such as the presence or absence of different kinds of data, seemed to be more important.

Molecular Identification and Pathogenicity of Diaporthe eres and D. hongkongensis (Diaporthales, Ascomycota) Associated with Cherry Trunk Diseases in China.

This study aimed to identify fungal species associated with trunk diseases of sweet cherries (Prunus avium) in several commercial cherry orchards in Beijing, Guizhou and Shandong provinces, China. In total, eighteen fungal strains that fitted well into the species concept of Diaporthe were isolated. Based on both morphological and multi-locus phylogenetic analyses of internal transcribed spacer region (ITS), beta-tubulin (tub-2), calmodulin (Cal) and translation elongation factor 1-α (tef1-α) sequencing data, fourteen isolates were identified as Diaporthe eres, while four isolates were classified as D. hongkongensis. Here, we report D. hongkongensis causing sweet cherry branch dieback disease and, further, we confirmed the host association of D. eres with sweet cherries in China. A pathogenicity assay revealed the ability of both D. eres and D. hongkongensis to cause shoot necrosis and stem lesions on Prunus avium cv. 'Brooks' (mean lesion lengths of 1.86 cm and 1.56 cm, respectively). The optimal temperature for the growth of both Diaporthe species was tested. The optimal growth temperature for D. hongkongensis was 30 °C, and the 25-28 °C temperatures were the most favorable for the growth of D. eres strains. This research advances the understanding of fungal trunk diseases in fruit crops, particularly gummosis and branch dieback disease in Chinese cherry orchards, and will aid growers in making decisions about cultural practices and disease management.

Acknowledging more biodiversity without more species

Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets (“genomic taxonomy”), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.

Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.

The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.

Detection of a PCR‐based mating type for native intraspecific Beauveria bassiana isolates

AbstractThis study developed a PCR‐based mating‐type analysis of 30 intraspecific Beauveria bassiana isolates after ITS phylogenetic analysis. Out of 30 isolates, only 11 B. bassiana isolates, viz., Bb4, Bb5, Bb11, Bb18, Bb19, Bb20, Bb23, Bb25, Bb27, Bb28, and Bb29, exhibited amplification of the mating‐type loci and were thought to be heterothallic. All of these isolates, with the exception of Bb20, had MAT1 mating‐type amplification. All these 11 isolates were clustered together with the MAT1‐ and MAT2‐specific reference strains of B. bassiana in the maximum likelihood phylogenetic analysis of mating‐type genes (IFO 31953 and IFO 31676, respectively). Although the PCR products obtained by the mating‐type assay were short, the phylogenetic trees of the mating‐type genes gave better resolution than that of the ITS region. Understanding the mating type of fungi can clarify the biological species concept and the identification of sex‐related genes in fungi without the presence of teleomorphs. So, combining phylogenetic, developmental, and mating research on each teleomorph specimen has the potential to clarify the systematics of Beauveria species.

What are Lycogala confusum and L. exiguum? Revising authentic collections of myxomycetes in the light of a molecular-aided species concept

What are Lycogala confusum and L. exiguum? Revising authentic collections of myxomycetes in the light of a molecular-aided species concept

Animalista, Narco-Cultural, Conservacionista. Visions of Nature Around the Case of Hippos in Colombia

AbstractSince their introduction in Colombia in the '80s for Pablo Escobar’s extravagant zoo, hippos have become an ecological problem around the basin of the Magdalena River. This article proposes an ecosemiotic discourse analysis of different visions of nature enacted by stakeholders and public opinion around the management of hippos in Colombia. Concretely, we focus on three particular discourses and visions of nature: animalista, narco-cultural, and conservacionista. In this article, we present the relevant social and ecological context of Colombia, the visions of nature theory and the impact of such visions on conservation measures regarding so-called invasive species; we describe and analyze the three visions of nature we center on, and present a computational analysis of discourse dynamics and controversies in Twitter between of such visions of nature; and we reflect on possible courses of action and recommendations about addressing the close interrelation of public discourses and ecosystem conservation by proposing an alternative view, based on the biosemiotic framework of semiocide, to the concept of invasive species.

Beyond overlap: Considering habitat preference and fitness outcomes in the umbrella species concept.

Umbrella species and other surrogate-species approaches to conservation provide an appealing framework to extend the reach of conservation efforts beyond single species. For the umbrella species concept to be effective, populations of multiple species of concern must persist in areas protected on behalf of the umbrella species. Most assessments of the concept, however, focus exclusively on geographic overlap among umbrella and background species, and not measures that affect population persistence (e.g., habitat quality or fitness). We quantified the congruence between the habitat preferences and nesting success of a high-profile umbrella species (greater sage-grouse, Centrocercus urophasianus, hereafter "sage-grouse"), and three sympatric species of declining songbirds (Brewer's sparrow Spizella breweri, sage thasher Oreoscoptes montanus, and vesper sparrow Pooecetes gramineus) in central Wyoming, USA during 2012 - 2013. We used machine-learning methods to create data-driven predictions of sage-grouse nest-site selection and nest survival probabilities by modeling field-collected sage-grouse data relative to habitat attributes. We then used field-collected songbird data to assess whether high-quality sites for songbirds aligned with those of sage-grouse. Nest sites selected by songbirds did not coincide with sage-grouse nesting preferences, with the exception that Brewer's sparrows preferred similar nest sites to sage-grouse in 2012. Moreover, the areas that produced higher rates of songbird nest survival were unrelated to those for sage-grouse. Our findings suggest that management actions at local scales that prioritize sage-grouse nesting habitat will not necessarily enhance the reproductive success of sagebrush-associated songbirds. Measures implemented to conserve sage-grouse and other purported umbrella species at broad spatial scales likely overlap the distribution of many species, however, broad-scale overlap may not translate to fine-scale conservation benefit beyond the umbrella species itself. The maintenance of microhabitat heterogeneity important for a diversity of species of concern will be critical for a more-holistic application of the umbrella species concept.

The Reactive Species Interactome in Red Blood Cells: Oxidants, Antioxidants, and Molecular Targets.

Beyond their established role as oxygen carriers, red blood cells have recently been found to contribute to systemic NO and sulfide metabolism and act as potent circulating antioxidant cells. Emerging evidence indicates that reactive species derived from the metabolism of O2, NO, and H2S can interact with each other, potentially influencing common biological targets. These interactions have been encompassed in the concept of the reactive species interactome. This review explores the potential application of the concept of reactive species interactome to understand the redox physiology of RBCs. It specifically examines how reactive species are generated and detoxified, their interactions with each other, and their targets. Hemoglobin is a key player in the reactive species interactome within RBCs, given its abundance and fundamental role in O2/CO2 exchange, NO transport/metabolism, and sulfur species binding/production. Future research should focus on understanding how modulation of the reactive species interactome may regulate RBC biology, physiology, and their systemic effects.

Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran.

During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30T (=IRAN 4042CT=CBS 149737T).

New shortcut for conservation: The combination management strategy of “keystone species” plus “umbrella species” based on food web structure

In our protection efforts, it is urgently needed to adopt precise and efficient management measures to address the challenges brought by biodiversity loss. Keystone and umbrella species are one of the most widely used surrogate species concepts. Keystone species often determine the stability of food web. Umbrella species, often the top predators and further influencing the integrity of the food web. Conservation efforts relying on a single surrogate species often face limitations. In order to seek complementary and optimized management strategies, we innovatively combining the concepts of two surrogate species, propose the hypothesis that “keystone species plus umbrella species reflect the stability and integrity of the food web respectively, so the combination of them is the most suitable combination for the overall protection of the food web”, and conducted validation research in a typical herbaceous marsh ecosystem. We constructed a typical food web model by using stable isotope, centrality indices and umbrella species strength index were used to quantitatively determine the keystone and umbrella species. Finally, we randomly paired nodes within the food web and remove different node pairs to investigate the impact of removal on the robustness of the food web, further validate the hypothesis. Our results indicated that when the node pair of “aquatic insects (keystone species) and top predatory catfish (Silurus asotus) (umbrella species)” was removed, the network efficiency reached its lowest point. This result confirmed our hypothesis, proposed a novel combination management strategy, which contribute to the development of more efficient and comprehensive biodiversity conservation decisions.

The Charophytes (Charophyceae, Characeae) from Dagestan Aquatic Habitats, North Caucasus: Biogeographical and Barcoding Perspectives

The charophytes in many regions of the world are still poorly understood. This hampers the synthesis of distributional and ecological datasets at worldwide and continental scales, as well as complicates the generalization of species concepts for widely distributed and local taxa. To fill in the blanks for charophytes in the Caucasus and to improve our knowledge of species distribution areas in Eurasia, a field survey and study of available specimens from Dagestan (North Caucasus, Russia) was conducted based on morphological observation using light and scanning electron microscopy and molecular genetic analyses allowing for the precise identification and testing of the presence of cryptic and undescribed taxa. Nineteen new localities for seven Chara species and one Tolypella species, seven new species, and one new genus were identified in the studied region, and one new species in the Caspian Sea region was found. Some species records changed the outline or filled in the gaps in species distribution data. The presence of species distributed mainly in central Eurasia (C. globata, C. neglecta) with mainly Mediterranean–Middle Eastern species (C. gymnophylla) is notable for this region, as well as for other studied regions of the Caucasus characterized by a mixture combination of species with different distribution patterns. Chara gymnophylla was frequent in Dagestan, similar to the Mediterranean and Middle Eastern regions. Small brackish waterbodies on the coast of the Caspian Sea, freshwater mountain rivers, small associated waterbodies, and water reservoirs are the main habitats of charophytes in the studied region. Based on habitat preference and distribution in the Caucasus, recommendations for the protection of some species were suggested. The lack of endemic species among charophytes from Dagestan and Caucasus contrasts with the flora of terrestrial magnoliophytes that is rich in species endemism.

New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.

The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.

Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota).

The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella. The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella. Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale. The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.

Conceptual sphere of phraseologisms of monetary relations in Ukrainian and Polish language cultures

The article examines the features of verbalization and the ways of conceptualizing cross-language phraseological equivalents and analogs in the field of monetary relations based on the material of Polish and Ukrainian lexicographic sources. Both structural and linguosemiotic methods of finding cross-linguistic phraseological parallels – „from meaning to form“ and „from form to meaning“ used in this research proved their effectiveness. The first method helped collect linguistic material and analyze phraseological equivalents and analogues of the conceptual sphere of monetary relations, which acquire additional attribution in translation, are metaphorically reinterpreted in the code of intangible values or material low-level values, form synonymous series with variant-characteristics and reflect common Slavic traditional folk imagery. By employing the method of correlation of the worldview and lexical semantics, the method of the thematic principle of language material distribution I built a linguistic and cultural model of the conceptual sphere of monetary relations of closely related ethnic groups. The core of the conceptual sphere contains the folk-poetic proto-concept wealth, the generic concept pieniądze / money, the related species concept small payment means and the historical concepts gold, silver, metal. The main space of the conceptual sphere of monetary relations is occupied by the anthropic sphere (the conceptualization of national character traits, extra-national anthropic types, a person’s appearance and biological characteristics, the most necessary physical and material things, such as food, clothing, housing, work, and spiritual ones, such as beliefs. On the periphery of the conceptual sphere of monetary relations there are linguistic and cultural concepts which designate economic phenomena and cosmocentric characteristics of existence. The linguosemiotic method of searching for linguistic material “from form to meaning”, helped describe a special type of cross-language phraseological units, which demonstrate “non-monetary” semantics, but receive such a formal expression that in one language is associated with the sphere of monetary relations, and in the other one causes lacunarity.

Towards elucidating species diversity of European inlandStrigamia(Chilopoda: Geophilomorpha): a first reassessment integrating multiple lines of evidence

AbstractStrigamia centipedes are widespread in European forest soils. However, a complex and inconsistent taxonomy has developed over time. Based on a modern species concept, we evaluated multiple lines of evidence for speciation among inland populations of Strigamia from the Italian region to the Baltic region, across central Europe. Hypotheses of species delimitation were drawn independently from: (1) morphological differentiation, by means of model-based cluster analyses of 52 specimens, after controlling for allometry and sexual dimorphism; (2) syntopy of morphologically distinct individuals, assumed to be representatives of coexistent species, from > 700 sites; and (3) molecular differentiation, by various methods applied to cytochrome c subunit I sequences of the same 52 specimens. Diagnoses and geographical distributions were revised by re-examining > 2000 specimens and the entire literature. We found preliminary evidence for: a Strigamia acuminata species complex, widespread, including a candidate species from the Eastern Alps differing in the forcipules; a Strigamia carniolensis species complex, hitherto often called Strigamia crassipes, widespread south of the Alps but absent from Sicily; a Strigamia crassipes species complex, hitherto often called Strigamia transsilvanica, more widespread than previously known, including three candidate species co-occurring in the Western Alps and differing in body size and the number of legs despite little genetic divergence; and Strigamia engadina, exclusive to a narrow part of the Central Alps.

Identifying ‘climate keystone species’ as a tool for conserving ecological communities under climate change

AbstractAimClimate change affects ecological communities via impacts on species. The community's response to climate change can be represented as the temporal trend in a climate‐related functional property that is quantified using a relevant functional trait. Noteworthy, some species influence this response in the community more strongly than others.InnovationLeveraging on the concept of keystone species, we propose that species with a strong effect on the community's functional response to climate change beyond their relative abundance can be considered as ‘climate keystone species’. We develop a stepwise tool to determine species' effects on a community's climate response and identify climate keystone species. We quantify the species‐specific effect by measuring the difference in the community's climate response with and without the species. Next, we identify climate keystone species as those with a strong residual effect after weighting with their relative abundances in the community.Main ConclusionsTo illustrate the use of the stepwise tool with empirical data, we identify climate keystone species that have a strong effect on the change in the average temperature niche in North American bird communities over time and find the identification tool ecologically relevant. Identification of climate keystone species can serve as an additional conservation method to efficiently protect ecological communities and, in turn, the ecosystem functions they provide.

A Taxonomic Revision of Arapatiella (Fabaceae: Caesalpinioideae): An Endemic and Threatened Genus from the Brazilian Coast

Arapatiella is a genus of Fabaceae (Leguminosae) of the subfamily Caesalpinioideae, endemic to the Atlantic Forest on the coast of the Brazilian state of Bahia. Popularly known in its region of occurrence due to the commercial use of its wood, Arapatiella is subject to strong influence of anthropic action. Currently, two species of trees are described for the genus: Arapatiella psilophylla and Arapatiella emarginata. However, the circumscription of these taxa is based on old works made with reduced sets of specimens, in need to be stronger delimited. Given this, we conducted a taxonomic and nomenclatural review of the genus based on an integrative species concept. We examined 125 gatherings from 26 national and international herbaria and living individuals collected during in situ expeditions. From the herbarium and field analyses, it was possible to state that the previous taxa circumscriptions do not fully correspond to the currently available specimen set and aren’t strong enough to delimit two species. Therefore, we chose to recombine the species as two varieties: Arapatiella psilophylla var. psilophylla and Arapatiella psilophylla var. emarginata, separated mainly by leaflet apex, stipule size, pubescence, and size of inflorescences and flowers. Distribution maps, taxonomic comments, an identification key, and a nomenclatural revision, including two new lectotypifications, are presented.