Phylogenetic Species Concept Research Articles

Molecular Characterisation and Phylogenetic Analysis of Dermatophytic Fungi Isolated from Tinea Capitis in Northwest Nigeria Using Sequence of the 28S rRNA

The detection and identification of fungal DNA from clinical samples is one of the fundamental approaches in biomedicine. The incidence, distribution, and control of dermatophytes has progress significantly and the use of phylogenetic species concepts based on rRNA regions have enhanced the taxonomy of dermatophyte species; however, the use of 28S rDNA genes has certain limitations. This gene has been used in dermatophyte taxonomy with limited enumeration; we appraised the sequence disparity within and among groups of the species, the gene ranking in identification, phylogenetic analysis, and taxonomy of 32 strains of eight dermatophyte species. In this study, a set of primers was adopted to amplify the target followed by a partial sequencing of the rDNA. The utilization of a pairwise nucleotide differentiation, an affinity was observed among eight dermatophyte species, with disparity among species ranging from 0 to 197 base pair (bp). Intra-species bp differences were found within strains of Trichophyton eriotrephon, Trichophyton bullosum, Trichophyton simii (Trichophyton genus), Microsporum audouinii, and Trichophyton tonsurans (Microsporum and Trichophyton genus, respectively); however, only some strains of Trichophyton eriotrephon were found to be invariant having three genotypes. Trichophyton tonsurans exhibited most intra-species variability. The characterization and construction of a phylogenetic tree of 28S rDNA gene on dermatophyte species provide a bedrock of an additional finding of connections between species. However, 28S rRNA capture provides a novel method of effective and sensitive detection of dermatophytes lodged in human skin scale. We report for the first time the emergence of T. eriotrephon, T. bullosum, T. simii, T. benhamiae, and Ctenomyces serratus dermatophytes from Tinea capitis in Nigeria.

Elevation of two subspecies of Dunnock Prunella modularis to species rank

The Western Palearctic endemic Dunnock Prunella modularis was recently revealed to comprise three distinct genetic lineages, each distributed in different Pleistocene refugia. Specifically, one is isolated in the Iberian refugium, another is confined to the Caucasus refugium, and the third is distributed in both the Italian and Balkan refugia, as well as across broader Europe. There is a probable absence of gene flow between the refugia. Analysis of plumage and song characteristics reveals robust differences between the Iberian subspecies P. m. mabbotti, Caucasian P. m. obscura and nominate P. m. modularis. Our assessments, in conjunction with genetic isolation, support species recognition under the Phylogenetic, Biological and Comprehensive Biological Species Concepts, via qualitative and quantitative criteria, and diagnosability. We thus propose the elevation of Iberian Dunnock P. mabbotti and Caucasian Dunnock P. obscura to species level.

Mycotoxin Production in Fusarium According to Contemporary Species Concepts.

Fusarium is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. Fusarium species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with Fusarium diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of Fusarium genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributedamong species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus Fusarium and how mycotoxin risk aligns with current phylogenetic species concepts.

DNA Barcoding And Species Delimitation Of Pyrausta (Lepidoptera: Crambidae, Pyraustinae) With Some Populations In Turkey

Pyrausta aurata (Scopoli, 1763), P. despicata (Scopoli, 1763), P. sanguinalis (Linnaeus, 1767), P. castalis (Treitschke, 1829), P. pavidalis (Zerny in Osthelder, 1935) and P. gulpembe (Kemal & Koçak, 2018) from Turkey were first time barcoded in the present study. Turkish populations and new species P. tatarica (Kemal, Kızıldağ & Koçak, 2020) were evaluated the phylogenetic positions with other Pyrausta species and populations. In the phylogenetic tree based on the mtCOI gene region delimitation of species and populations constructed with Neighbor-joining, Bayesian inference, and maximum-likelihood algorithms. For understanding the importance of the phylogenetic species concept in species delimitation, was reviewed cladistic topology and genetic distances of Pyrausta species with new data.

A slippery reality: the epistemological shifting sands of tokogeny, phylogeny, lineages and species delimitation

This essay provides an alternative perspective on the history of classification, species and subspecies concepts to that presented in a recent review by Padial and de la Riva. Central points of difference relate to Darwin’s role in revolutionizing classification, Willi Hennig’s role in the development of the phylogenetic species concept, the metaphysics and epistemology of species as lineage segments, the true history of the subspecies concept, and the impact of large amounts of genetic data on the accuracy and precision of species/subspecies delimitation. Possession of a clear understanding of the history of systematics, and a chronology of which ideas inform which other ideas, provides critical background knowledge to build a sound conceptual framework for interpreting the nuances of phylogenetic evidence today. A glossary of potentially unfamiliar terms is included as an appendix.

<strong><em>Spiranthes bightensis</em> (Orchidaceae), a New and Rare Cryptic Hybrid Species Endemic to the U. S. Mid-Atlantic Coast</strong><em></em>

Recognizing species diversity is challenging in genera that display interspecific similarity and intraspecific variation; hybridization and the evolution of cryptic hybrid species amplifies these challenges. Recent molecular and morphological research focused on the systematics of Spiranthes (Orchidaceae) support hybrid speciation as an important driver of species diversity, particularly within the S. cernua species complex. Working under an integrated history-bound phylogenetic species concept, new molecular and morphometric data provide evidence for a new and rare cryptic hybrid species resulting from the ancient hybridization of S. cernua × S. odorata, here described as S. bightensis. Although S. bightensis is regionally sympatric with S. cernua it does not co-occur with that species, and it is allopatric with respect to S. odorata. Endemic to a narrow region extending from the Delmarva Peninsula to Long Island, New York, this new species occurs in the shadow of the Northeast megalopolis and appears to have undergone a major population decline over the last 200 years. By recognizing this distinct evolutionary lineage as a new species, this research is the first step towards developing conservation protocols for this rare species and highlights the importance of the North American Geologic Coastal Plain for biodiversity conservation and evolution.

The life cycle and field epidemiology of Uromycladium acaciae (Pucciniales) on Acacia mearnsii in South Africa

AbstractUromycladium acaciae has damaged plantations of Acacia mearnsii in southern Africa since 2013. Uredinia of a species of Uromycladium have been known on A. mearnsii in South Africa since the 1980s. However, the recent damage is associated with telia and spermogonia. Uredinia and telia were previously treated as conspecific with a phylogenetic species concept. However, uredinia did not form after previous artificial inoculation experiments with teliospores. Controlled studies identified the optimum conditions for basidiospore infection, but the optimum conditions for sporulation and dispersal have not been identified. To investigate the life cycle and field epidemiology of Uromycladium on A. mearnsii, spores were trapped weekly and development of disease symptoms and plant phenology were monitored monthly at three plantations. Telia and spermogonia developed independently from uredinia, and nucleotide polymorphisms between rDNA of uredinia and telia were fixed based on high throughput sequencing and PCRs. All three weather variables measured had a significant effect on teliospore abundance at two of the three sites. Teliospore abundance was greatest during trapping periods when mean relative humidity was high, mean rainfall was 4–5 mm day−1 and mean temperature was 15–16°C. Teliospore counts peaked at the end of summer, potentially the result of epidemic build‐up. Results support the hypothesis that despite sharing a most recent common ancestor, uredinia on A. mearnsii in southern Africa are independent to the life cycle of the telial rust, which likely constitutes a new introduction. Furthermore, teliospores of U. acaciae disperse under wet conditions, and the wet season between October and March is the optimal period for wattle rust development.

Molecular phylogeny and species delimitation of the genus Tonkinacris (Orthoptera, Acrididae, Melanoplinae) from China.

Tonkinacris is a small group in Acrididae. While a few species were occasionally sampled in some previous molecular studies, there is no revisionary research devoted to the genus. In this study, we explored the phylogeny of and the relationships among Chinese species of the genus Tonkinacris using the mitochondrial COI barcode and the complete sequences of ITS1 and ITS2 of the nuclear ribosomal DNA. The phylogeny was reconstructed in maximum likelihood and Bayesian inference frameworks, respectively. The overlap range between intraspecific variation and interspecific divergence was assessed via K2P distances. Species boundaries were delimitated using phylogenetic species concept, NJ tree, K2P distance, the statistical parsimony network as well as the GMYC model. The results demonstrate that the Chinese Tonkinacris species is a monophyletic group and the phylogenetic relationship among them is (T. sinensis, (T. meridionalis, (T. decoratus, T. damingshanus))). While T. sinensis, T. meridionalis and T. decoratus were confirmed being good independent species strongly supported by both morphological and molecular evidences, the validity of T. damingshanus was not perfectly supported by molecular evidence in this study.

Broad and narrow host ranges in resolved species of Cintractia limitata s. lat. (Anthracoideaceae, Ustilaginomycotina) on Cyperus

Cintractia (Anthracoideaceae, Ustilaginomycotina) is a widespread genus of smut fungi that parasitizes species of Cyperaceae. Specimens of Cintractia spp. on species of Cyperus s. lat. were examined to resolve their taxonomy, including a species on Cyperus aromaticus, which is an invasive weed in Australia. A phylogenetic species concept was used to show that Cintractia limitata s. lat. contains three different species, Cintractia limitata, C. tangensis, and a new species C. kyllingae. The proposed taxonomy is based on phylogenetic analyses of the ITS rDNA region and on the position of the sori in diverse parts of inflorescences examined in approximately 100 specimens of Cintractia. A morphological synapomorphy in C. tangensis is sori with firmly agglutinated spore masses around the base of the peduncles, rarely in the spikelets. Cintractia limitata forms powdery spore masses between flowers and is known only to occur on Cyperus species with spikelets in capitate heads. Cintractia kyllingae was found on Cy. aromaticus and may have potential as a biological control agent in Australia.

Haploporus (Basidiomycota, Polyporales) in sub-Saharan Africa: Poria eichelbaumii, a long-forgotten name, is reinstated in Haploporus and H. grandisporus sp. nov. is proposed

Poria eichelbaumii, a long-forgotten name, is transferred to Haploporus based on studies of the type specimen, comparison with new collections, and evidences from both morphology and phylogeny. The species is redescribed and illustrated. Haploporus grandisporus is described as new, on the basis of concordant morphological and phylogenetic species concepts. These two species form two very closely related clades within the Haploporus lineage in [28S-ITS]-based phylogenetic inferences. Haploporus eichelbaumii and H. grandisporus are distinguished by the size of their basidiospores (11.5–14.5 × 5.0–6.0 μm, average = 12.7 × 5.8 μm, vs 14–17.5 × 6.0–7.3 μm, average 15.4 × 6.6 μm), the size of their pores (2.5–3.5 / mm, vs 1.5–2.5 / mm), and, likely, divergent autecologies. Although both species occur in montane ecosystems of the eastern African rift, the data so far available suggest they occupy different habitats. Haploporus eichelbaumii has wider distribution, spanning over both branches of the eastern rift, at elevation ~ 1500–2500 masl, in various vegetation types, mostly on small-sized dead branches or twigs, and dead bamboo culms. It is known so far from Kenya, Tanzania, and Malawi to the East, and western Burundi, western Uganda, and Eastern Congo (DRC) in the Albertine mountain ranges. Haploporus grandisporus is known, hitherto, only from the Eastern slopes of Mount Elgon in Kenya, at the timberline, 2900–3200 masl, mostly on dead heather branches (Erica arborea, Ericaceae) in heather thickets. Haploporus nanosporus is currently the third known Haploporus species from tropical Africa, known from the western edge of the Guineo-Congolian rain forest in Gabon and Cameroon. This species is also redescribed and illustrated.

<strong>A revision of <em>Hierochloe</em> sect. <em>Monoecia</em> (Anthoxanthinae, Pooideae, Poaceae)</strong>

We propose a new taxonomic arrangement for the South American species of Hierochloe sect. Monoecia, based on a recently published study combining morphological, molecular and cytological data. Only four out of the eight commonly accepted species of this section (H. pusilla, H. juncifolia, H. quebrada and H. redolens pro parte) are recognised using both phylogenetic (apomorphic) and phenetic species concepts. The four remaining species (H. altissima, H. gunckelii, H. spicata and H. utriculata) are reduced to varieties of the widespread H. redolens due to weak molecular, macro- and micromorphological differentiation. These varieties are presented here as new taxonomical combinations: H. redolens var. gunckelii, H. redolens var. spicata, H. redolens var. utriculata and H. redolens var. altissima. Lectotypes are designated for the names H. pusilla, H. juncifolia, H. redolens var. utriculata, and H. redolens var. altissima.

Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria.

The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).

Accounting for clinal variation and covariation in the assessment of taxonomic limits: why we should remember the ‘rules’

Accounting for clinal variation and covariation in the assessment of taxonomic limits: why we should remember the ‘rules’

Towards Genomic Criteria for Delineating Fungal Species.

The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%—and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed—not as the only criterion—but as an additional tool in the versatile toolbox of fungal taxonomy.

Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence.

Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.

Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus).

The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double‐digest restriction site‐associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.

<p class="HeadingRunIn"><strong>A revision of <em>Attalea</em> (Arecaceae, Arecoideae, Cocoseae, Attaleinae)</strong></p>

A taxonomic revision of the neotropical palm genus Attalea based on morphological data was carried out. Nine hundred and two herbarium specimens were scored for 21 quantitative and 33 qualitative variables. Using the Phylogenetic Species Concept, qualitative variables were used to recognize 30 species. These are widely distributed in Central and South America from Mexico to Bolivia and Paraguay, with one species in Haiti. Nomenclature, descriptions, and distribution maps are provided for each species. Qualitative variables are illustrated, and illustrations of 22 living plants are also provided.

<p class="HeadingRunIn"><strong>A revision of <em>Calamus</em> (Arecaceae, Calamoideae, Calameae, Calaminae)</strong></p>

A revision of Calamus was carried out based on morphological data. Eight thousand, six hundred and thirty-three herbarium specimens were examined and scored for 14 quantitative and 157 qualitative variables. Application of the Phylogenetic Species Concept to 516 preliminary species of Calamus resulted in recognition of 411 phylogenetic species. Of these, 38 are recognized as new (C. barisanensis, C. brevissimus, C. brunneus, C. calciphilus, C. densifloropsis, C. disjunctus, C. divergens, C. exiguus, C. furvus, C. gaharuensis, C. goramensis, C. heteracanthopsis, C. hosensis, C. impressus, C. insolitus, C. insularis, C. johanis, C. kinabaluensis, C. kubahensis, C. latus, C. lengguanii, C. lobatus, C. notabilis, C. obiensis, C. oresbiopsis, C. oxleyoides, C. pahangensis, C. powlingii, C. saltuensis, C. seropakensis, C. spinosus, C. sulawesiensis, C. tambingensis, C. tapanensis, C. trigynus, C. vinaceus, C. viridis, C. wedaensis). Analysis of quantitative variables and geographic distributions resulted in the division of 11 species into 36 subspecies. Eight species were considered to be ochlospecies (C. erioacanthus, C. inermis, C. javensis, C. melanochaetes, C. micranthus, C. moseleyanus, C. plicatus, C. siphonospathus). Nomenclature, descriptions, and distribution maps are provided for all species. Images of the type specimens of all new species are provided as well as images of most qualitative variables. One hundred and forty–three species are illustrated with images from living plants.

Giraffe taxonomy, geographic distribution and conservation

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Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses.

Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of aquatic plants, possesses extremely variable morphology and the presence of cryptic diversity makes its classification problematic. Previous studies have revealed cryptic Ottelia species in Asia, but very little is known about the molecular systematics of this genus in Africa, a center of species diversity of Ottelia. In this study, we sampled Ottelia ulvifolia, an endemic species of tropical Africa, from Zambia and Cameroon. We used six chloroplast DNA regions, nrITS and six polymorphic microsatellite markers to estimate the molecular diversity and population genetic structure in O. ulvifolia. The phylogenetic inference, STACEY and STRUCTURE analyses supported at least three clusters within O. ulvifolia, each representing unique flower types (i.e., bisexual yellow flower, unisexual yellow flower and bisexual white flower types). Although abundant genetic variation (> 50%) was observed within the populations, excessive anthropogenic activities may result in genetic drift and bottlenecks. Here, three cryptic species of O. ulvifolia complex are defined, and insights are provided into the taxonomy of Ottelia using the phylogenetic species concept.