Intraspecific Genetic Variation Research Articles

Intraspecific genetic diversity and coexistence in phytoplankton populations

AbstractThe past two decades have seen a drastic increase in the availability and use of genetic techniques to study phytoplankton communities. As a result, it is now well documented that phytoplankton populations are genetically diverse, despite predominantly asexual reproduction and minute morphological variation. Genetic variation can lead to variation also in phenotype, and some traits vary more among genotypes than between species. Trait‐based approaches tackle this by focusing on traits rather than on species. However, trait‐based models often have difficulty predicting and explaining the huge trait‐diversity among coexisting individuals competing for the same few resources. Thus, we ask the question: How do hundreds, if not thousands, of genotypes coexist in a highly competitive environment? In this review, we gather information on genetic and phenotypic variations in coexisting genotypes and elaborate on three mechanisms by which broad intraspecific genetic diversity may be possible: neutral mutations, environmental fluctuations, and trade‐offs among traits. These have all been applied on an interspecies level, and we discuss their use also among coexisting genotypes. We find that genetic diversity to be almost exclusively studied in blooming species and that clonal diversity frequently measure above 0.95 (i.e., 95% of individuals sampled are genetically different). Genetic diversity seems stable throughout blooms, suggesting that competitive exclusion is low or that new genetic material is frequently being introduced into populations. Further, we find high intraspecific trait‐variation in several key traits among coexisting strains but also that trait‐variation is often neglected in studies on phytoplankton, making coexistence difficult to predict.

Spatial conservation planning of forest genetic resources in a Mediterranean multi-refugial area

The Kunming-Montreal Global Biodiversity Framework recognised the urgency of taking action to conserve intraspecific genetic diversity (IGD) as an insurance against habitat degradation and environmental change. Recent work suggests that 90–99 % of IGD should be conserved to safeguard viability of future generations.Here, we addressed such a conservation issue in three forest tree species in Italy: silver fir (Abies alba Mill.), Heldreich's pine (Pinus heldreichii H. Christ), and pedunculate oak (Quercus robur L.). We used microsatellite markers to measure IGD of 36 (A. alba), 15 (P. heldreichii) and 25 (Q. robur) natural sites, including several putative glacial refugia. We developed a spatial conservation planning (SCP) analysis to quantify the genetic irreplaceability of each site and identify the minimum set coverage ensuring IGD protection. Finally, we compared SCP results with the contributions to allelic diversity within and between sites, total allelic diversity and private allelic richness.We found that between 44 % and 73 % of sites were required to conserve 90–99 % of the alleles, and that this conservation effort held even when targeting lower percentages of alleles to protect (50–75 %). Glacial refugia were often included in the minimum set coverage, confirming biogeographical expectations. Finally, sites with high genetic irreplaceability were found to have higher private allelic richness on average. These results are discussed in the light of the biogeographic history of the species studied and the current policies for the conservation of forest genetic resources.

New records of Micromegistus bakeri, Trägårdh 1948 (Acari: Mesostigmata: Parantennulidae), a mite symbiotic on carabid beetles, and notes on the species’ distribution and host specificity

Micromegistus bakeri is a purported commensal mite that spends most of its life on the ground beetle Scarites subterraneus. It is thought to sustain itself by feeding on the beetle’s dermal fluids and opportunistically scavenging on nearby organic debris, although the nature of this relationship, and whether it’s beneficial, detrimental or neutral to the host, is unclear. This species has previously been recorded in Mississippi, Texas, and Kansas. This study reports the first record of M. bakeri in Pennsylvania based on our collecting, as well as the first records for Ohio, Michigan, Missouri, Arizona, and Canada, based on previously unpublished museum records. The literature and our own survey of carabid beetles indicate that M. bakeri has a strong preference for S. subterraneus as a host and is not common on other carabids. Our own data shows a prevalence of 27% of S. subterraneus (10 out of 37) carrying M. bakeri, with an average of 3.1 (range 1–8) mites per infested beetle; none of the other 31 carabid species collected during this study carried M. bakeri. This study represents the first publicly available COI barcode sequence for this taxon. We also provide photographs of live mites and summarize suspected sightings from additional locations across North America obtained via the citizen science websites BugGuide and iNaturalist. These records indicate that M. bakeri is present throughout the known distribution of its beetle host. Suspected M. bakeri were observed on other Scarites species in North America, but their presence on these hosts needs to be confirmed via examination of physical specimens. It should be noted that the westernmost record for the species is in Arizona, based on a male specimen that exhibits 6.6% divergence in COI barcode sequence with specimens from Pennsylvania. The specimen is otherwise essentially morphologically identical to males of eastern USA, and it is therefore uncertain whether it represents a cryptic species or merely high intraspecific genetic divergence over a large geographic distance.

High-quality chromosome-level genome assembly of Nicotiana benthamiana

Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.

Geometric morphometrics to differentiate species and explore seasonal variation in three Mansonia species (Diptera: Culicidae) in central Thailand and their association with meteorological factors.

Mansonia mosquito species are recognised as a significant vector of human pathogens, primarily transmitting the filarial nematode, Brugia malayi. In central Thailand, the three most prevalent Mansonia species are Mansonia annulifera, Mansonia indiana and Mansonia uniformis. This study explored the influence of seasonal changes on the phenotypic variation of these Mansonia species in central Thailand using the geometric morphometrics (GM). To ensure accurate species identification, we integrated GM techniques with DNA barcoding, examining distinctions in both phenotype and genotype among the species. The intraspecific genetic divergence ranged from 0.00% to 1.69%, whereas the interspecific genetic divergence ranged from 10.52% to 16.36%. The clear distinction between intra- and interspecific distances demonstrated the presence of a barcoding gap, confirming the successful differentiation of the three Mansonia mosquito species through DNA barcoding. Similarly, the interspecies GM assessment for classifying Mansonia species demonstrated a high degree of accuracy, with an overall performance of 98.12%. Exploring seasonal variation in the three Mansonia species revealed wing variations across different seasons, and pronounced variations appearing in the cool season. Regarding their association with meteorological factors, Ma. annulifera and Ma. uniformis showed significant positive correlations with temperature (p < 0.05), and Ma. uniformis also displayed a significant negative correlation with atmospheric pressure (p < 0.05). The insights from this study will deepen our understanding of the adaptive patterns of Mansonia mosquitoes in Thailand's central region, paving the way for enhanced disease surveillance related to these vectors.

Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842).

Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.

Surveillance for Selected Pathogens and Parasites of Northern Bobwhite (Colinus virginianus) from Western Oklahoma, USA, 2018-20.

The Northern Bobwhite (Colinus virginianus) has been undergoing a range-wide population decline. Potential causes for declines across its historic range have been investigated for decades and include habitat loss and fragmentation and a variety of parasitic and infectious diseases. Although there have been studies on bobwhite ecology in Oklahoma, USA, relatively little is known about parasites and pathogens in the region. We evaluated the health of free-ranging bobwhites from nine sites in western Oklahoma. From 2018 to 2020, 206 bobwhites were evaluated for gross and microscopic lesions and tested for selected pathogens. In general, bobwhites were in good nutritional condition with ample muscle mass and fat stores. No significant gross lesions were observed in any bobwhite and no significant histologic lesions were detected in a subset. There was no evidence of infection with or exposure to reticuloendotheliosis virus, West Nile virus, respiratory Mycoplasmataceae species, Pasteurella multocida, intestinal Eimeria spp., or oral Trichomonas spp. Several pathogens of potential concern were detected, including avian adenovirus (8.6%), Toxoplasma gondii (2.3%), and haemosporidians (a Haemoproteus sp. (1.5%), Leucocytozoon schoutedeni (1.5%), and Plasmodium homopolare haplotype 2 [lineage LAIRI01; 3.6%]). Physaloptera sp. (12%) and Sarcocystis sp. (1%) were detected in the breast muscle. Low intraspecific genetic diversity was noted for Physaloptera sp., and sequences were most similar to Physaloptera sequences from bobwhites and grasshoppers (Orthoptera) in Texas. Low intensities of chewing lice, chiggers, and ticks were observed. A subset of bobwhites had evidence of exposure to selected toxicants and heavy metals; a small number had low levels of iron, manganese, zinc, molybdenum, and copper, which were not considered diagnostically relevant. In general, bobwhites from western Oklahoma appeared to be in good health with a low diversity of pathogens detected, but future work is needed to understand potentially changing disease risks for this population.

Evaluating different approaches to integrate genome-wide genetic diversity in spatial conservation prioritization

Locations for new protected areas should be identified with consideration of intraspecific genetic diversity because genetic variation enhances the adaptability of species to novel environmental conditions. The process of siting new protected areas is called spatial conservation prioritization and is often formulated as a mathematical problem to be solved with the aid of computer software. Integrating multidimensional continuous metrics of genome-wide genetic diversity in spatial conservation prioritization involves significant challenges in terms of computation speed and memory requirements. In this study, we tested and compared several approaches to approximate the multidimensional continuous metrics of genetic diversity using multidimensional discrete genetic clusters or unidimensional discrete conservation features. To this end, we applied two tools for spatial conservation prioritization, raptr and prioritizr, to genomic datasets of two fish species (the white seabream Diplodus sargus and the red mullet Mullus surmuletus) sampled throughout most of their distribution range in the Mediterranean Sea. We found that most of the approximations tested either did not achieve all genetic conservation targets or resulted in excessively high conservation costs. Nonetheless, approaches based on multidimensional genetic clusters allowed generating prioritizations with relatively small gaps in genetic objectives at very high computation speed. This might be an interesting option for exploratory or interactive analyses such as those performed in workshop with stakeholders.

Three new species and one new record of Deimatidae (Echinodermata, Holothuroidea, Synallactida) discovered in the South China Sea and the Mariana fore-arc area using integrative taxonomic methods.

Deep-sea holothurian specimens were collected during five scientific expeditions (2018-2023) using the submersible vehicle 'Shenhaiyongshi'. Our examination of specimens of Deimatidae from the South China Sea and the Mariana fore-arc area revealed three new species, which were described as Oneirophantaidsseicasp. nov., Oneirophantabrunneannulatasp. nov., and Oneirophantalucernasp. nov. These species were distinguished from each other and from congeners by the arrangement, and number of ventrolateral tube feet and ossicle types. We also reported Oneirophantamutabilismutabilis Théel, 1879 for the first time from the Mariana fore-arc area, and we recorded Deimavalidumvalidum for the second time from the South China Sea. The taxonomy of these new species and new records is discussed, and a phylogenetic analysis based on a concatenated dataset of 16S and COI genes was conducted. Additionally, the inter- and intraspecific genetic divergences we calculated among deimatid species. The results support the assignment of these new species to the genus Oneirophanta and their separation from congeners. A description of the main morphological characters of Oneirophanta species is also provided. The data were collected from geographically diverse areas and suggest that species of Deimatidae were abundant in the Pacific Ocean and occupied a wide range of depths.

A DNA barcode library of Austrian geometridae (Lepidoptera) reveals high potential for DNA-based species identification.

Situated in the Eastern section of the European Alps, Austria encompasses a great diversity of different habitat types, ranging from alpine to lowland Pannonian ecosystems, and a correspondingly high level of species diversity, some of which has been addressed in various DNA barcoding projects. Here, we report a DNA barcode library of all the 476 species of Geometridae (Lepidoptera) that have been recorded in Austria. As far as possible, species were sampled from different Austrian regions in order to capture intraspecific genetic variation. In total, 2500 DNA barcode sequences, representing 438 species, were generated in this study. For complete coverage of Austrian geometrid species in the subsequent analyses, the dataset was supplemented with DNA barcodes from specimens of non-Austrian origin. Species delimitations by ASAP, BIN and bPTP methods yielded 465, 510 and 948 molecular operational taxonomic units, respectively. Congruency of BIN and ASAP partitions with morphospecies assignments was reasonably high (85% of morphospecies in unique partitions), whereas bPTP appeared to overestimate the number of taxonomic units. The study furthermore identified taxonomically relevant cases of morphospecies splitting and sharing in the molecular partitions. We conclude that DNA barcoding and sequence analysis revealed a high potential for accurate DNA-based identification of the Austrian Geometridae species. Additionally, the study provides an updated checklist of the geometrid moths of Austria.

Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique

The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations.

Sibling species of the major malaria vector Anopheles gambiae display divergent preferences for aquatic breeding sites in southern Nigeria

Background When integrated with insecticide-treated bed nets, larval control of Anopheles mosquitoes could fast-track reductions in the incidence of human malaria. However, larval control interventions may deliver suboptimal outcomes where the preferred breeding places of mosquito vectors are not well known. This study investigated the breeding habitat choices of Anopheles mosquitoes in southern Nigeria. The objective was to identify priority sites for mosquito larval management in selected urban and periurban locations where malaria remains a public health burden. MethodsMosquito larvae were collected in urban and periurban water bodies during the wet-dry season interface in Edo, Delta, and Anambra States. Field-collected larvae were identified based on PCR gel-electrophoresis and amplicon sequencing, while the associations between Anopheles larvae and the properties and locations of water bodies were assessed using a range of statistical methods.ResultsMosquito breeding sites were either man-made (72.09%) or natural (27.91%) and mostly drainages (48.84%) and puddles (25.58%). Anopheles larvae occurred in drainages, puddles, stream margins, and a concrete well, and were absent in drums, buckets, car tires, and a water-holding iron pan, all of which contained culicine larvae. Wild-caught Anopheles larvae comprised Anopheles coluzzii (80.51%), Anopheles gambiae sensu stricto (s.s.) (11.54%), and Anopheles arabiensis (7.95%); a species-specific PCR confirmed the absence of the invasive urban malaria vector Anopheles stephensi among field-collected larvae. Anopheles arabiensis, An. coluzzii, and An. gambiae s.s. displayed preferences for turbid, lowland, and partially sunlit water bodies, respectively. Furthermore, An. arabiensis preferred breeding sites located outside 500 m of households, whereas An. gambiae s.s. and An. coluzzii had increased detection odds in sites within 500 m of households. Anopheles gambiae s.s. and An. coluzzii were also more likely to be present in natural water bodies; meanwhile, 96.77% of An. arabiensis were in man-made water bodies. Intraspecific genetic variations were little in the dominant vector An. coluzzii, while breeding habitat choices of populations made no statistically significant contributions to these variations.ConclusionSibling malaria vectors in the An. gambiae complex display divergent preferences for aquatic breeding habitats in southern Nigeria. The findings are relevant for planning targeted larval control of An. coluzzii whose increasing evolutionary adaptations to urban ecologies are driving the proliferation of the mosquito, and An. arabiensis whose adults typically evade the effects of treated bed nets due to exophilic tendencies.

High genetic load without purging in caribou, a diverse species at risk

High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.

Spatial genetic structure in European marbled newts revealed with target enrichment by sequence capture

European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group because morphological data show geographical variation and because the Iberian Peninsula is a recognized center of speciation and intraspecific genetic diversity for all kinds of organisms, amphibians included. We use target enrichment by sequence capture to generate c. 7 k nuclear DNA markers. We observe limited genetic exchange between the species, which confirms their distinctiveness. Both species show substantial genetic structuring that is only in part mirrored by morphological variation. Genetically differentiated groups are found in the south (T. marmoratus) and west (T. pygmaeus) of the species ranges. Our observations highlight the position of the Iberian Peninsula as a hotspot for genetic differentiation.

Intraspecific morphological and genetic variation in South African populations of a polystomatid flatworm parasite

The African Clawed Frog Xenopus laevis, a global invader, exhibits a marked phylogeographic divergence among native populations in southern Africa, which seems to enhance its invasive potential. The polystomatid flatworm, Protopolystoma xenopodis, is the frog’s most frequently co-introduced metazoan parasite. In an integrative approach, we utilised morphometrics and molecular markers to assess variation in P. xenopodis in its native range. We measured twelve key morphological characters from 23 flatworms and compared these statistically between flatworms collected from the northern- and southernmost distribution in South Africa. Phylogenetic analyses were based on three concatenated markers, namely 28S and 12S rDNA and COX1, from six flatworms. The combination of five morphological characters, which involve egg size, gut morphology and size of the attachment hooks, differentiated northern and southern populations of P. xenopodis. The multilocus phylogenetic analyses showed a cluster of northern P. xenopodis and two southern lineages with more basal positioning. These findings demonstrate a relatively high level of intraspecific variation in P. xenopodis in its native range. The presented intraspecific variation of P. xenopodis could be potentially informative to trace geographic origin in its non-native range.

Variation in RNA interference sensitivity in the southern pine beetle, Dendroctonus frontalis (Coleoptera: Curculionidae)

Abstract Intraspecific genetic variation underpins many evolutionary processes and phenomena. For species considered pests, the dynamics of how genetic variation is distributed geographically take on a greater importance, because they can impact pest-management strategies directly. This is particularly true when management strategies are genetic in nature, such as population manipulation via RNA interference (RNAi; a naturally occurring antiviral response that disrupts translation of messenger RNAs into proteins to silence genes). Using RNAi for gene silencing is highly species specific; however, the efficacy of this approach in geographically distinct populations of widespread pest species has not been evaluated comprehensively. Here, we present a preliminary study evaluating differential susceptibility of geographically disparate populations of southern pine beetle, Dendroctonus frontalis, to RNAi. Although the efficacy of RNAi has been demonstrated in localized populations, D. frontalis has a broad distribution across North and Central America and is expanding its range owing to climate change. We observe differences in response between and within geographically distinct populations from its core range and recently expanded range. Our findings have broad implications for the use of RNAi as a management tool in widely distributed species and highlight the need for a deeper understanding of intraspecific genetic variation in this species and others.

Caenorhabditis elegans immune responses to microsporidia and viruses

The model organism Caenorhabditis elegans is susceptible to infection by obligate intracellular pathogens, specifically microsporidia and viruses. These intracellular pathogens infect intestinal cells, or, for some microsporidia, epidermal cells. Strikingly, intestinal cell infections by viruses or microsporidia trigger a common transcriptional response, activated in part by the ZIP-1 transcription factor. Among the strongest activated genes in this response are ubiquitin-pathway members and members of the pals family, an intriguing gene family with cross-regulations of different members of genomic clusters. Some of the induced genes participate in host defense against the pathogens, for example through ubiquitin-mediated inhibition. Other mechanisms defend the host specifically against viral infections, including antiviral RNA interference and uridylation. These various immune responses are altered by environmental factors and by intraspecific genetic variation of the host. These pathogens were first isolated 15 years ago and much remains to be discovered using C. elegans genetics; also, other intracellular pathogens of C. elegans may yet to be discovered.

DNA barcoding of Notopterygii Rhizoma et Radix (Qiang-huo) and identification of adulteration in its medicinal services

Safety concerns, stemming from the presence of complex and unpredictable adulterants, permeate the entire industrial chain of traditional Chinese medicines (TCMs). The Notopterygii Rhizoma et Radix (NReR) from the Apiaceae family, commonly known as “Qiang-huo”, is a widely used herbal medicine. The recent surge in its demand has given rise to a proliferation of counterfeit and substituted products in the market. Traditional identification presents inherent limitations, while DNA mini-barcoding, reliant on sequencing a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In this study, we constructed a comprehensive Internal Transcribed Spacer 2 (ITS2) matrix encompassing genuine NReR and their commonly found adulterants for the first time. Leveraging this matrix, we conducted a thorough assessment of the genetic profiles and sources of NReR available in the Chinese herbal medicine market. Following established DNA barcoding protocols, the intra-specific genetic divergences within NReR species were found to be lower than the inter-specific genetic divergences from other species. Among the 120 samples that were successfully amplified, ITS2 exhibits an outstanding species-level identification efficiency of 100% when evaluated using both the BLASTN and neighbor-joining (NJ) tree methods. We concluded that ITS2 is a mini-barcode that has shown its potential and may become a universal mini-barcode for the quality control of “Qiang-huo”, thereby ensuring the safety of clinical medication.

Genetic Diversity and DNA Barcoding of Thrips in Bangladesh.

Thrips are economically important pests, and some species transmit plant viruses that are widely distributed and can damage vegetables and cash crops. Although few studies on thrips species have been conducted in Bangladesh, the variation and genetic diversity of thrips species remain unknown. In this study, we collected thrips samples from 16 geographical locations throughout the country and determined the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene in 207 thrips individuals. Phylogenetic analysis revealed ten genera (Thrips, Haplothrips, Megalothrips, Scirtothrips, Frankliniella, Dendrothripoides, Astrothrips, Microcephalothrips, Ayyaria, and Bathrips) and 19 species of thrips to inhabit Bangladesh. Among these, ten species had not been previously reported in Bangladesh. Intraspecific genetic variation was diverse for each species. Notably, Thrips palmi was the most genetically diverse species, containing 14 haplotypes. The Mantel test revealed no correlation between genetic and geographical distances. This study revealed that thrips species are expanding their host ranges and geographical distributions, which provides valuable insights into monitoring the diversity of and control strategies for these pests.

Opsarius siangi, a new Chedrinae fish species from the Brahmaputra drainage, India

Opsarius siangi sp. nov., a previously undocumented species, has been identified from Siang River, Pasighat, Arunachal Pradesh, India. This newly described species is distinguished by a suite of unique morphological characteristics, notably including a complete lateral line, consisting of 65–77 scales, 32–39 pre-dorsal scales, 12–15 scales positioned between dorsal fin origin and lateral line, presence of two pairs of barbels, body depth ranging from 18.80% to 27.42% of standard length and a distinct pattern of 8–15 vertical bars adorning the body. A comprehensive genetic analysis was conducted by scrutinizing 78 Cytochrome oxidase I (COI) sequences extracted from Chedrinae fishes, with particular focus on Opsarius and Barilius genera. Phylogenetic analysis revealed that O. siangi sp. nov. occupies a distinctive clade, displaying close affinity with O. shacra. Intraspecific K2P genetic divergence, assessed at 0.02, falls well within established species delineation thresholds, while interspecific divergence in comparison to O. shacra was recorded at 0.112. Complementary species delimitation methodologies, including BIN and bPTP, further underscore taxonomic uniqueness of O. siangi sp. nov., within Chedrinae family. This description enriches our understanding of biodiversity within Siang River ecosystem and underscores the merit of employing multi-pronged approaches in taxonomic investigations.