Taxonomic Implications Research Articles

Unveiling hidden diversity: Phylogenomics of neotomine rodents and taxonomic implications for the genus Peromyscus

Neotomine rodents (Cricetidae, Neotominae) represent one of the most commonly encountered and diverse group of rodents in North America, yet phylogenetic relationships within this group remain uncertain. This subfamily is known for its rapid evolution, adding more complexity to our efforts to unravel their evolutionary history. The main debate revolves around the recognition of the genus Peromyscus as monophyletic or paraphyletic due to its relationship with other genera such as Habromys, Megadontomys, Podomys, Neotomodon, and Osgoodomys. Here, we aim to resolve phylogenetic relationships within Neotominae, to further explore their evolutionary history and taxonomic boundaries. We used target capture and high-throughput sequencing of complete mitogenomes and thousands of genome-wide ultraconserved elements loci (UCEs). Our comprehensive analyses encompassed 53 species of Neotominae spanning 12 previously described genera, along with one yet-undescribed genus. We also investigated 12 out of the 13 species groups within Peromyscus. Our analyses, including Maximum Likelihood and Bayesian Inference with both mitogemomes and UCEs, as well as the coalescent species-tree-based approach with UCEs, consistently recovered concordant and well-resolved phylogenies with high levels of nodal support. We identified seven main clades within Neotominae that could potentially be recognized at the generic level, mostly to categorize the genus Peromyscus as a monophyletic group, including one species group within “Peromyscus”. Furthermore, our divergence dating estimates place the crown age of Neotominae to be around the late Miocene at ca. 7.9 – 10.7 mya. While generic level diversification continued through the Pliocene, species level diversification predominantly occurred during the late Pliocene, extending through the Pleistocene and Holocene. These epochs have been recognized as periods with significant changes in flora and fauna, driving ecological transformations on a global scale. We hypothesized that climatic and vegetation shifts during the Neogene and Quaternary, coupled with geological events, topographical features, and the presence of biogeographical corridors played a pivotal role in the speciation and diversification of Neotominae. Recognizing the importance of generating genomic-scale data coupled with a broad taxonomic sampling, our study, for the first time, offers resolution of the relationships among the main lineages of Neotominae. We expect that the phylogeny presented here will serve as a foundational resource for future systematic and evolutionary studies. This includes facilitating a proper comprehensive taxonomic revision of the group and the formal description and naming of new genera.

Exploring the Anomala fuscosignata-complex: discovery of two new species from southern China (Coleoptera: Scarabaeidae: Rutelinae).

An investigation towards taxonomy of the Anomala fuscosignata-complex from southern China and northern Vietnam was conducted through direct morphological comparison and molecular phylogenetic analysis, which results in discovery of two new species: A. nanlingensis Zhao, Zorn & Liu, sp. nov. and A. zhengyucheni Zhao, Zorn & Liu, sp. nov. The morphological differences in female genitalia and low genetic divergence as well as their taxonomic implications within Anomalini are discussed.

A new species and genus of Lower Jurassic rhynchonellide (Brachiopoda) from Livari (Rumija Mountain, Montenegro): taxonomic implications of the shell microstructure

ABSTRACT A new rhynchonellide brachiopod genus and species, Skadarirhynchia semicostata gen. et sp. nov., is described from the late Pliensbachian of Livari, Rumija Mountain, southeastern Montenegro. It occurs in shallow-water brachiopod-crinoid packstone beds (bioclastic limestones) of the periplatform facies of the Dinaric Carbonate Platform. Stratigraphy is constrained by means of 87Sr/86Sr dating indicating a late Pliensbachian age, and by the fact that the brachiopod beds lie immediately below the Toarcian marly limestones, which is consistent with the regional stratigraphical position. The new species has a circular to roundly pentagonal outline and semicostate shells with 10‒12 strong angular ribs. Internally, it shows reduced dental plates, narrow and thin hinge plates inclined dorsally with small crural bases, crescent-like and laterally convex, and hamiform crura. The shell microstructure of the new taxon is characterised by a homogeneous secondary layer (a single layer with no sublayers) built of rhombic fibres that are typically of coarse-fibrous type (eurinoid pattern) 35‒50 μm wide and 20‒30 μm thick. Other co-occurring rhynchonellide species such as Prionorhynchia fraasi and Cuneirhynchia dalmasi are also described. Shell microstructures for the genus Cuneirhynchia are presented.

Phylogeography of the Sinica Group of Macaques in the Himalayas: Taxonomic and Evolutionary Implications.

Owing to the taxonomic incongruence between the morphological features and genetic relationships of the sinica group of macaques (genus Macaca), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (Macaca munzala) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the sinica group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies M. assamensis assamensis and the western subspecies M. a. pelops) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The sinica group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the sinica group of macaques.

Morphological diversity and taxonomic implications of seedling structures in selected species of Fabaceae from Karachi (Pakistan)

Seedling morphology is a valuable tool for plant identification and classification, particularly in early growth stages. This study investigates the morphological characters of seedlings from randomly selected taxa within the Fabaceae family, focusing on cotyledons, first two leaves, and subsequent leaves to support taxonomic differentiation. Not all subfamilies within Fabaceae are fully represented in this study. Seedlings from 14 randomly selected taxa were analyzed using morphological traits such as cotyledon shape, phyllotaxy, leaf shape, and venation patterns. An artificial key was constructed, and three dendrograms were developed based on cotyledon morphology, first two leaves, and subsequent leaves to illustrate taxonomic relationships. Statistical analyses were employed to assess clustering patterns among the taxa. The artificial key categorized the taxa into subfamilies within Fabaceae, including Caesalpinoideae, Mimosoideae, and Papilionoideae, based on cotyledon shape and leaf morphology. Dendrogram analysis revealed distinct clustering patterns, grouping species according to key morphological features. Not all subfamilies of Fabaceae were covered, but the analysis provided clear separation among the species studied. The morphological traits observed were consistent with previous taxonomic findings and offered a reliable basis for classification. The morphological features of seedlings, especially cotyledons and eophylls, serve as reliable taxonomic markers for identifying and classifying species within Fabaceae. Although the study does not encompass all subfamilies, the randomly selected taxa demonstrated clear taxonomic distinctions. Dendrograms combined with artificial keys provided a useful framework for classification. Further studies should expand the scope to include more taxa, covering all subfamilies of Fabaceae. Integrating molecular and other taxonomic tools such as anatomy, cytology, and chemistry can enhance the precision of classification frameworks and provide deeper insights into the evolutionary relationships within the family.

First report of ultra-sculpturing and taxonomic implications of seed morphology of selected genus Euphorbia L

First report of ultra-sculpturing and taxonomic implications of seed morphology of selected genus Euphorbia L

The cardamom conundrum resolved: Recircumscription and placement of Elettaria in the only pantropically distributed ginger lineage

AbstractThe overarching aim of the present study is to sort out the taxonomy of a group of gingers that include the useful and worldwide economically important green cardamom, Elettaria cardamomum, and its wild relatives, to highlight potentially overlooked genetic resources. These species occur naturally in India and Sri Lanka, and our study facilitates more appropriate management priorities for the remaining forest fragments in which they occur. We used NGS Hyb‐Seq methods and sampled four species of the Alpinia I (Fax) clade, six representatives of Aframomum and Renealmia as well as two other basally flowering Sri Lankan species. This is the only pantropically distributed lineage within the entire family, and our result shows that the Alpinia I clade in fact is simply the genus Elettaria (confined to India and Sri Lanka), which is sister to the genera Aframomum (Africa) and Renealmia (Africa and Neotropics). The taxonomic implications are: (1) a recircumscription of Elettaria comprising seven species (E. cardamomum, E. ensal, E. floribunda, E. involucrata, E. rufescens as well as two new species, E. facifera and E. tulipifera described here); (2) the Sri Lankan endemic genus Cyphostigma should be retained; (3) the new monotypic genus, Srilankanthus endemic in Sri Lanka, is described with S. nemoralis, formerly Amomum nemorale, as type. A key is provided to the seven species of Elettaria and lectotypifications are made for five species (Cyphostigma pulchellum, Elettaria floribunda, E. involucrata, E. nemoralis, E. rufescens).

Foliar LM and SEM Insights: Investigating Epidermal Features and Its Taxonomic Implications in Some Verbenaceae Taxa

Foliar LM and SEM Insights: Investigating Epidermal Features and Its Taxonomic Implications in Some Verbenaceae Taxa

A new approach to the fossil flamingo from Pie de Vaca locality (Puebla, central México) and some taxonomic and biogeographic implications

Pie de Vaca is a late Cenozoic site located in the municipality of Tepexi de Rodríguez, Puebla, Mexico. It is known for its ichnofossil record including footprints of camelids, carnivores, and peccaries, as well as the taphoglyph of an almost complete flamingo skeleton. This fossil specimen was previously identified as Phoenicopterus stocki, a small extinct species, through linear osteometric comparisons of the tibiotarsus. This study presents new data on the morphological features of the taphoglyph skull impression. The extant genera Phoenicopterus, Phoenicoparrus, and Phoeniconaias differ in the morphology and size of the skulls. The fossil specimen analyzed exhibits a small head and a distinct cranial shape when compared to those genera. The results confirm that the taphoglyph belongs to an adult of a small phenicopterid. The two-dimensional morphometric comparisons of the tibiotarsus based on the ratio of distal depth to distal width shows that the taphoglyph is larger than Phoeniconaias minor and Phoenicopterus minutus, and more similar to Phoenicopterus ruber. The analysis revealed previously unknown characteristics of the taphoglyph and refutes its previous identification as the extinct species Phoenicopterus stocki. The specimen appears to be a small adult flamingo, but it differs from known extant genera. These findings confirm the presence of a group of small flamingos in the late Cenozoic of North America and Mexico, with the most complete specimen being the taphoglyph of Pie de Vaca. However, further research remains necessary to establish its connections with extinct and extant phenonicopterids.

Intergeneric Comparison of Staminal Trichomes in the Tribe Ipomoeeae (Convolvulaceae).

Hairs or trichomes distributed on the base of filaments in the morning glory family, known as staminal trichomes, differ from those found on other plant parts and have been recognized for their taxonomic value for over a century. In this study, our aim was to investigate the appearance of staminal trichomes in the tribe Ipomoeeae Hall. f., a significant tribe within the family Convolvulaceae, and assess their taxonomic implications. Micromorphological examinations were conducted using clearing techniques on 73 taxa from seven out of eight genera within the tribe, and the data were analyzed using factor analysis of mixed data (FAMD). The results show that, among all examined taxa, only two species lacked staminal trichomes. Glandular staminal trichomes were the most common type observed, and they were the only type observed in Ipomoea, Paralepistemon, Rivea, Stictocardia, and most Argyreia species. Nonglandular staminal trichomes were restricted to Astripomoea, Lepistemon, and some Argyreia taxa. The glandular trichomes in Ipomoea exhibited the largest variation and overlapped with other glandular trichome-bearing genera. However, genera with nonglandular trichomes were readily distinguishable from each other. Both glandular and nonglandular trichomes were basically composed of a stalk and apical cell, yet they varied in shape, size, density, and distribution pattern. This study provides a detailed examination and application of microscale features, emphasizing the significance of micromorphology in plant taxonomy.

Morphology of hemipenes and its taxonomic implication in the fused eyelids species of the genus Ablepharus (Squamata: Scincidae)

The representatives of the genus Ablepharus Fitzinger, 1824 have not been studied in detail from a morphological and taxonomic perspective. The morphology of hemipenes of 14 taxa of the fused eyelids species of the genus was studied. Manual eversion and inflation with absolute ethanol was used for preparation of the organs. The results indicate that the Ablepharus hemipenes show little variation in general shape and main structures: all hemipenes are deeply bifurcated, without large external calcified or keratinous spines or similar structures. Based on hemipenial morphology, the studied taxa can be separated into two clades: 1) with long, slender and 2) with short, robust lobes of the hemipenis. The morphology of this structure demonstrates close relationships between the fused eyelids ablepharine skinks, points out unresolved taxonomic problems, and shows general congruence with available molecular phylogenies. Hemipenial characteristics appear to be a useful tool for the identification of the species within the genus. Problems associated with the real taxonomic status of the Ablepharus budaki anatolicus paratypes and the distribution of other taxa are discussed. The morphology of the hemipenis of the family Scincidae and the related, inconsistent use of terminology are also commented on.

Taxonomic implications of the leaf anatomy of twelve species of Senna ser. Bacillares (Leguminosae) from northeastern Brazil

Taxonomic implications of the leaf anatomy of twelve species of Senna ser. Bacillares (Leguminosae) from northeastern Brazil

Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy.

South American coca (Erythroxylum coca and E. novogranatense) has been a keystone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half-century, global demand for its alkaloid cocaine has driven intensive agriculture of this plant and placed it in the center of armed conflict and deforestation. To monitor the changing landscape of coca plantations, the United Nations Office on Drugs and Crime collects annual data on their areas of cultivation. However, attempts to delineate areas in which different varieties are grown have failed due to limitations around identification. In the absence of flowers, identification relies on leaf morphology, yet the extent to which this is reflected in taxonomy is uncertain. Here, we analyze the consistency of the current naming system of coca and its four closest wild relatives (the "coca clade"), using morphometrics, phylogenomics, molecular clocks, and population genomics. We include name-bearing type specimens of coca's closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the statistical analyses illuminate that rounder and more obovate leaves of certain varieties could be associated with the subtle domestication syndrome of coca. Our phylogenomic data indicate extensive gene flow involving E. gracilipes which, combined with morphometrics, supports E. gracilipes being retained as a single species. Establishing a robust evolutionary-taxonomic framework for the coca clade will facilitate the development of cost-effective genotyping methods to support reliable identification.

Morphometric Variation in the Red-Cheeked Mud Turtle (Kinosternon cruentatum) and its Taxonomic Implications

Morphometric Variation in the Red-Cheeked Mud Turtle (Kinosternon cruentatum) and its Taxonomic Implications

Craniomandibular osteology and the first record of the ocular skeleton in a South American rhynchosaur (Archosauromorpha, Hyperodapedontinae)

A new rhynchosaur specimen from the Upper Triassic (Candelária Sequence) of Southern Brazil is presented in this contribution. While these reptiles constitute some of the most sampled fossils from these beds, their taxonomic, phylogenetic, and palaeobiological status remain understudied. Delving into the cranial elements of the new specimen we performed a taxonomic and phylogenetic assessment, assigning it to “Hyperodapedon” sanjuanensis, a form that occurs in Brazil and Argentina. This assignment was based on distinctive craniomandibular features such as the absence of lingual teeth in the dentary, a unique feature among hyperodapedontine rhynchosaurs. Furthermore, our phylogenetic analysis supports this scenario. Our approach emphasizes the broader need for comprehensive anatomical descriptions of South American rhynchosaurs, particularly in Brazil, where some crucial taxa remain undescribed and/or unfigured. This study also reinforces the need for a revision of the clade Hyperodapedontinae and the Hyperodapedon genus. The orbital region of the new specimen reveals delicate scleral ossicles, presenting a unique window into the visual adaptations and habits of these reptiles. This is the first record of the ocular skeleton for a rhynchosaur of South America. Beyond the taxonomic and phylogenetic implications, this study elucidates the role of the ocular skeleton in regards to sensory adaptations in hyperodapedontine rhynchosaurs.

Leaf Anatomy Structure of Codiaeum variegatum (L.) Rumph. ex A. Juss Cultivars

Codiaeum variegatum (L.) Rumph. ex a. Juss is a common ornamental plant with a high variation of leaves shape and colour. This study aimed to analyze the leaves’ anatomy and the phenetic relationship between eight cultivars of C. variegatum which were defined by the differences in leaf morphology. The paraffin method prepared the transversal section of leaves, and anatomical characters were converted into binary data to calculate the similarity coefficient which was analyzed by Numerical Taxonomy System (NTSYS) 2.1 version. Leaves of eight cultivars of C. variegatum are varied in the anatomical structure of the primary vein and lamina. The eight cultivars of C. variegatum were clustered into four. The variations were found in 19 primary vein and lamina anatomy characteristics and the similarity coefficient is up to 0.59 between all cultivars. It can be concluded that the combination of leaf anatomical structures and midrib anatomical characters have notable taxonomic implications for future research.

Anatomy and micromorphology of Tilia species from Turkey and its taxonomic implication.

The genus Tilia L. belongs to Malvaceae and it is represented by four species in Turkey. These are T. cordata, T. platyphyllos, T. rubra subsp. caucasica, and T. tomentosa. Tilia species have medicinal importance, especially to treat colds, flu, and coughs, and are also used as sedatives. Inflorescence with bract is recorded in the pharmacopeia as used parts. This study aimed to investigate the differences in leaf and bract characteristics in distinguishing Tilia species. Leaves and bracts were examined anatomically and micromorphologically under light and scanning electron microscopes (LM and SEM). There is no comparative anatomical and micromorphological study of Tilia species from Turkey. Microscopic examination allows for the observation of stomata types, trichomes, and other anatomical structures. These features can vary among species and can aid in differentiation. Features of bract that is medicinally used part were evaluated to find efficient diagnostic characters. The leaves also possess distinct characteristics, and leaf morphology is already used in the identification key in Flora. The emphasis is on identifying the species of medically used drugs. A diagnostic key was created using LM and SEM based on bract features to differentiate taxa for the first time. RESEARCH HIGHLIGHTS: Leaf and bract anatomy of Tilia taxa was studied via LM and SEM. The raw plant material is inflorescence with bract so identification by bract is important for species adulteration. An diagnostic key based on bract features was created for the first time.

Taxonomic implications of pollen morphological features for taxa identifications: plant–honeybees interactions

Taxonomic implications of pollen morphological features for taxa identifications: plant–honeybees interactions

Systematic Implications of Palynomorph Diversity Using Microscopic Trends Among Asteraceous Flora From the Drylands of Baluchistan, Pakistan.

Pollen micromorphological traits with taxonomic implications are first reported from the study area for 50 Asteraceous taxa belonging to nine tribes. Cichorieae (21 taxa), Cardueae (11 taxa), Inuleae (six taxa), and Anthemideae (four taxa) are the leading tribes. The research included Cousinia haeckeliae, Himalaiella afghana, Pterachaenia stewartii (endemic to Afghanistan and Pakistan), and Xylanthemum macropodum (endemic to Baluchistan). Light and scanning electron microscopy were employed for the visualization of pollen photomicrographs. The data was analyzed statistically via SPSS, PAST, and Origin. Significant diagnostic qualitative and quantitative palynological traits were explored for discrimination down to the species level within the tribes. All the investigated taxa possessed radial symmetry, isopolarity, and monad form (characters for distinction at the subdivision level). The aperture types were trizonocolporate, tetrazonocolporate, and tricolporate with number position and character (NPC) formulas N3P4C5, N4P4C5, and N3P4C3. Goniotreme, peritreme, and ptychotreme types of amb were recognized. Echinate, echinate lophate, scabrate, and gemmate sculpturing were present with and without perforated surface patterns. Variations in the shapes in polar and equatorial views and lacuna shapes further assisted the separation of taxa. The observed shape classes were perprolate, prolate spheroidal, prolate, subprolate, oblate spheroidal, suboblate, and oblate. Principal component analysis, correlation, standard probability plots, and ridge line paired features plot for quantitative variables determined the positive correlation between the length and width of colpi in equatorial and polar view with polar axis and equatorial diameter and number of spines between colpi with the number of spines per pollen. The number of spines per pollen was negatively correlated with the width and length of colpi in the polar view. Multiple sample analysis of variance (ANOVA) concluded that a high statistically significant difference exists among the means of analyzed traits. The examined qualitative and quantitative palynological traits revealed noticeable variations, thus providing the source for species discrimination in Asteraceous tribes.

Geometric morphometry of the Rhodniusprolixus complex (Hemiptera, Triatominae): patterns of intraspecific and interspecific allometry and their taxonomic implications.

In the subfamily Triatominae, the genus Rhodnius is one of the most studied, not only because of its epidemiological importance, but also because of the difficulty in differentiating its species. Currently, one of the strategies to control Chagas disease, besides other initiatives such as the analysis of donated blood, is focused on fighting the vector. Correctly identifying triatomines is essential for the entomoepidemiological surveillance of Chagas disease. The objective of the present work was to compare the species of the R.prolixus complex using geometric morphometry of hemelytra and heads to evaluate the patterns of intraspecific and interspecific allometry and their taxonomic implications. This method can help in the diagnosis of close species, whose morphological characteristics are insufficient for correct identification. Specimens from five different collections were used, covering the species included in the R.prolixus complex (R.barretti, R.dalessandroi, R.domesticus, R.marabaensis, R.milesi, R.montenegrensis, R.nasutus, R.neglectus, R.neivai, R.prolixus and R.robustus). Morphometric analyses indicated that the hemelytra are not structures with good resolution for separating species and, for this reason, the use of the heads proved to be more adequate for this group (thus allowing differentiation of all species of the R.prolixus complex). The results suggest that R.milesi is a variant of R.neglectus and confirms that R.prolixus and R.robustus are distinct species. Furthermore, we propose the creation of the R.neivai complex comprising R.domesticus and R.neivai.