Intraspecific Distances Research Articles

DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia)

This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, Torrenticola soniae Pešić, sp. nov. and T. elisabethae Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Portugal now have reference barcodes in BOLD. High intraspecific distances were recorded for some species, suggesting the presence of cryptic diversity and species complexes that needs further study. Our results improve the DNA barcode reference database for Portuguese water mites, enhancing species identification accuracy and stimulating future investigation.

Molecular approach challenges the monophyly of the genus Benthana Budde-Lund, 1908 (Oniscidea, Philosciidae)

ABSTRACT Although new data and methodologies are gaining prominence in the field of taxonomy, the vast majority of terrestrial isopod species are still described solely based on morphology. The genus Benthana was recently revised and currently comprises 30 species found in South America. However, the broad geographic distribution of some species, coupled with the presence of few diagnostic characters, raises doubts about the validity of the described species. This study aimed to test the applicability of DNA Barcoding to assess the congruence between morphological and molecular identification of Benthana species. We analyzed 72 individuals belonging to 13 species from the scientific collection of the UFRGS Crustacean Laboratory. We obtained 24 sequences from ten Benthana species. The molecular phylogenies demonstrated that Benthana forms a paraphyletic group. Even at the species level, paraphyletic taxa were observed. Species delimitation methods revealed the presence of eight molecular entities within Benthana. Regarding genetic distances, we observed low intra-specific distances and significantly high inter-specific distances. Our results show that molecular analysis does not support the current taxonomy of Benthana. Therefore, a reassessment of the genus systematics based on integrative taxonomy is warranted.

DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang.

The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.

DNA barcoding of southern African mammal species and construction of a reference library for forensic application.

Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.

Genetic polymorphisms of common sandflies in selected areas of Henan Province based on DNA barcoding

To characterize the species of common sandflies in Henan Province using DNA barcoding with cytochrome c oxidase subunit I (COI) gene as the molecular marker, and to analyze the genetic polymorphisms of sandflies, so as to provide insights into visceral leishmaniasis prevention and control in Henan Province. Sandfly specimens were sampled from 13 sandflies surveillance sites from 2021 to 2023 in Anyang City, Zhengzhou, Luoyang and Xuchang cities (Zhengzhou-Luoyang-Xuchang areas) where visceral leishmaniasis cases were reported and in Jiaozuo and Xinxiang cities (Jiaozuo-Xinxiang areas) without visceral leishmaniasis cases reported. Genomic DNA was extracted from a single sandfly, and COI gene was amplified. The amplification product was subjected to bidirectional sequencing. Following sequence assembly, the species of sandflies was characterized through sequence alignment using the BLAST tool. The intra-specific and inter-specific genetic distances of sandflies were estimated among different areas using the software Mega 11, and phylogenetic trees were created. The polymorphisms of nucleotide sequences in the sandflies COI gene were estimated using the software DnaSP. The fixation index (FST) of different geographical isolates of sandflies was calculated using the Arlequin software, and the gene flow value (Nm) was used to measure the gene flow in the sandflies populations. In addition, the population genetic structure of different geographical populations of Phlebotomus chinensis was analyzed using the STRUCTURE software. A total of 978 sandflies were collected from 13 sandflies surveillance sites in Zhengzhou-Luoyang-Xuchang areas, Jiaozuo-Xinxiang areas and Anyang City of Henan Province from 2021 to 2023, and 475 sandflies were randomly sampled for subsequent detections. A total of 304 Ph. chinensis, 162 Se. squamirostris and 9 Se. bailyi were identified based on molecular biological detection of the COI gene, and Se. bailyi was reported for the first time in Henan Province. The intraspecific genetic distances of sandflies were 0.000 to 0.040, and the inter-specific genetic distances ranged from 0.133 to 0.161. Phylogenetic analysis revealed that each of the three sandfly species was clustered into a clade. The genetic polymorphisms of Ph. chinensis populations varied among different areas, with the highest haplotype diversity (0.966 ± 0.007) and the greatest nucleotide diversity (0.011) in Zhengzhou-Luoyang-Xuchang areas, and the lowest haplotype diversity (0.720 ± 0.091) and nucleotide diversity (0.004) in Anyang City. The dominant haplotype of Ph. chinensis populations was Pch_Hap_2 in Anyang City and Jiaozuo-Xinxiang areas, with moderate genetic differentiation (0.05 < FST < 0.15) and frequent gene exchange (Nm value > 1) between Ph. chinensis populations sampled from Anyang City, and Jiaozuo-Xinxiang areas. Population genetic structure analysis showed that the dominant component of Ph. chinensis populations was K5 in Anyang City and Jiaozuo-Xinxiang areas. No obvious dominant haplotype was observed in Ph. chinensis populations sampled from Zhengzhou-Luoyang-Xuchang areas, which had very high genetic differentiation (FST > 0.25) and little gene exchange (Nm value < 1) with Ph. chinensis populations from Anyang City, and Jiaozuo-Xinxiang areas, with K3 as the dominant component. In addition, there was no significant difference in the genetic polymorphism level among Se. squamirostris populations from the three areas. There are Ph. chinensis, Se. squamirostris and Se. bailyi in Henan Province, and S. bailyi is recorded for the first time in Henan Province by molecular biological assays. There are different levels of genetic differentiation and gene exchange among P. chinensis populations in different areas of Henan Province.

Growing bacterial colonies harness emergent genealogical demixing to regulate organizational entropy

Spatiotemporal organization of individuals within growing bacterial colonies is a key determinant of intraspecific interactions and colony-scale heterogeneities. The evolving cellular distribution, in relation to the genealogical lineage, is thus central to our understanding of bacterial fate across scales. Yet, how bacteria self-organize genealogically as a colony expands has remained unknown. Here, by developing a custom-built label-free algorithm, we track and study the genesis and evolution of emergent self-similar genealogical enclaves, whose dynamics are governed by biological activity. Topological defects at enclave boundaries tune finger-like morphologies of the active interfaces. The Shannon entropy of cell arrangements reduce over time; with faster-dividing cells possessing higher spatial affinity to genealogical relatives, at the cost of a well-mixed, entropically favorable state. Our coarse-grained lattice model demonstrates that genealogical enclaves emerge due to an interplay of division-mediated dispersal, stochasticity of division events, and cell-cell interactions. The study reports so-far hidden emergent self-organizing features arising due to entropic suppression, ultimately modulating intraspecific genealogical distances within bacterial colonies.

Applicability and perspectives for DNA barcoding of soil invertebrates

Belowground invertebrate communities are dominated by species-rich and very small microarthropods that require long handling times and high taxonomic expertise for species determination. Molecular based methods like metabarcoding circumvent the morphological determination process by assigning taxa bioinformatically based on sequence information. The potential to analyse diverse and cryptic communities in short time at high taxonomic resolution is promising. However, metabarcoding studies revealed that taxonomic assignment below family-level in Collembola (Hexapoda) and Oribatida (Acariformes) is difficult and often fails. These are the most abundant and species-rich soil-living microarthropods, and the application of molecular-based, automated species determination would be most beneficial in these taxa. In this study, we analysed the presence of a barcoding gap in the standard barcoding gene cytochrome oxidase I (COI) in Collembola and Oribatida. The barcoding gap describes a significant difference between intra- and interspecific genetic distances among taxa and is essential for bioinformatic taxa assignment. We collected COI sequences of Collembola and Oribatida from BOLD and NCBI and focused on species with a wide geographic sampling to capture the range of their intraspecific variance. Our results show that intra- and interspecific genetic distances in COI overlapped in most species, impeding accurate assignment. When a barcoding gap was present, it exceeded the standard threshold of 3% intraspecific distances and also differed between species. Automatic specimen assignments also showed that most species comprised of multiple genetic lineages that caused ambiguous taxon assignments in distance-based methods. Character-based taxonomic assignment using phylogenetic trees and monophyletic clades as criteria worked for some species of Oribatida but failed completely for Collembola. Notably, parthenogenetic species showed lower genetic variance in COI and more accurate species assignment than sexual species. The different patterns in genetic diversity among species suggest that the different degrees of genetic variance result from deep evolutionary distances. This indicates that a single genetic threshold, or a single standard gene, will probably not be sufficient for the molecular species identification of many Collembola and Oribatida taxa. Our results also show that haplotype diversity in some of the investigated taxa was not even nearly covered, but coverage was better for Collembola than for Oribatida. Additional use of secondary barcoding genes and long-read sequencing of marker genes can improve metabarcoding studies. We also recommend the construction of pan-genomes and pan-barcodes of species lacking a barcoding gap. This will allow both to identify species boundaries, and to cover the full range of variability in the marker genes, making molecular identification also possible for species with highly diverse barcode sequences.

Studies on Molecular Taxonomy and Morphological Characteristics of Haematobia irritans exigua (de Meijere, 1903); A New Range Extension in the Bargur Hills of Erode District in Tamil Nadu, India

The flies of the genus Haematobia (Diptera:Muscidae) are hematophagous ectoparasites of medical and veterinary importance. The morphological identification of these flies is often complicated due to their similarities. This was the first documentation of Haematobia irritans exigua in Tamil Nadu which affected free-ranging Bargur Cattle (Bos indicus) from Bargur Hills of Tamil Nadu. The aim of this research was to provide the details on the molecular characterization and molecular divergence of the cytochrome c oxidase subunit 1 gene (COI) and 28S Ribosomal RNA of Haematobia irritans exigua and to compare them with the morphological features. The results of this study showed that the nucleotide composition of the COI gene of Haematobia irritans exigua had a higher AT (69.5%) and a lower GC (30.4%). The rate of transition was higher than that of transversion. The intra-specific distance based on COI gene analysis did not exceed 1.1%, while the inter-specific distance between different species ranged from 0.9% to 14.1%. A neighbor-joining tree and an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree were constructed using 1000 bootstrapped samples to analyze the phylogenetic relationship between different muscidae species based on the COI gene as an identification marker. The analysis of 28S Ribosomal RNA showed an intra-specific distance of 1.6% and an inter-specific distance ranging from 1.49% to 8.56%. The 28S rRNA revealed the presence of intra-specific variation among the species. Additionally, this study found notable color variations on the thorax of the flies in the same population, along with a minute phenotypical variation with minimum intraspecific distance among the flies in the same population. This taxonomic data of the hematophagous fly Haematobia irritans exigua would be well-intentioned for identification.

Genetic and morphological evidence support the specific status of the endemic Ericaandevalensis (Ericales, Ericaceae).

Assessing the taxonomic status of closely related taxa is crucial in plant systematics and can have important implications for conservation and human plant use. Ericaandevalensis Cabezudo & Rivera is a metallophyte endemic species from highly metal-polluted soils of SW Iberian Peninsula, an area with a mining history going back more than 5,000 years. Ericaandevalensis is closely related to Ericamackayana Bab., a northern Iberian species also present in western Ireland. The status of E.andevalensis as a species or subspecies subordinated to E.mackayana is subject to debate. Here, we assessed the genetic and phenotypic relationship between both species, including the population structure of E.andevalensis. We used high throughput sequencing to determine genome-wide Single Nucleotide Polymorphisms (SNPs), and morphometric analyses from 35 reproductive and vegetative traits. The morphological analysis showed at least eight characters that can discriminate the two species, from which ovary hairiness and the size of leaf glandular hairs were the most informative. Genetic analyses showed that each species formed a monophyletic cluster with full support, separated by an interspecific genetic distance >4-fold higher than intra-specific distance. Population genetic analyses of E.andevalensis shows that populations are highly structured, with the Portuguese one as the most isolated and less variable. These results support the recognition of E.andevalensis as a distinct species with a highly constrained ecological requirements and a narrow geographic distribution, but with a limited gene flow between populations. We discuss the implications of these outcomes in conservation policies and potential uses of E.andevalensis such as decontamination of polluted soils.

Integrative studies of Microtus hartingi and Microtus guentheri (Cricetidae, Arvicolinae) and taxonomic problem of Microtus elbeyli

In this study, Taxonomic differences between Microtus guentheri and Microtus hartingi, which are similar in terms of external morphological features, were determined using linear morphometric, geometric morphometric, karyological and molecular analyses methods. Through classical morphometric (mean values) and geometric morphometric analyses of craniodental and mandible characters, influenced by various genetic, developmental, and functional processes, it was found that M. hartingi and M. guentheri exhibited notable differences in both mean linear measurements and shape. The Jackknife in classical morphometric analyses of samples, which underwent molecular and karyological species diagnoses, was higher than 88 % for each character. In geometric morphometric analyses, the Procrustes distance for shape follows the order Ventral < Dorsal < Mandible < M3<M2<M1. Based on cross-validation, the accurate classification rate is between 73 and 100 %. In both mean linear measurements and centroid size, M. hartingi specimens exhibited significantly larger mandibles and craniodentals compared to individuals of M. guentheri. According to PLS results, there was a significant relationship between the shape of M1, M2 and M3 and environmental variables, while the relationship between their size and environmental variables was not significant. However, neither the shape nor the size of the other parts had an sufficient relationship with environmental variables. Both species exhibited karyological similarity with a chromosome number of 2n = 54, but display polymorphism in chromosome arm number. There were differences in the C-banding of autosomal chromosomes and X chromosome. The classification of species in classical and geometric morphometric analyses, diverges from the outcomes of karyological and molecular assessments. In both species, the intraspecific genetic distance remained below 1.35 %. The cyt-b exhibits significant differentiation between the two species (K2P = 6.55 %). The divergence time for M. guentheri from the clade containing M. hartingi + M. qazvinensis + Microtus dogramacii was estimated to be 0.73 million years ago. Since no sample of Microtus elbeyli with karyological and cyt-b characteristics was found in the samples taken from the type locality, the taxonomic status of M. elbeyli remains unclear.

Delimiting species, revealing cryptic diversity in Molytinae (Coleoptera: Curculionidae) weevil through DNA barcoding.

The subfamily Molytinae (Coleoptera: Curculionidae), being the second largest group within the family Curculionidae, exhibits a diverse range of hosts and poses a serious threat to agricultural and forestry industries. We used 1,290 cytochrome c oxidase subunit I (COI) barcodes to assess the efficiency of COI barcodes in species differentiation and uncover cryptic species diversity within weevils of Molytinae. The average Kimura 2-parameter distances within species, genus, and subfamily were 2.90%, 11.0%, and 22.26%, respectively, indicating significant genetic differentiation at both levels. Moreover, there exists a considerable degree of overlap between intraspecific (0%-27.50%) and interspecific genetic distances (GDs; 0%-39.30%). The application of Automatic barcode gap discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and jMOTU resulted in the identification of 279, 275, 494, 322, 320, and 279 molecular operational taxonomic units, respectively. The integration of 6 methods successfully delimited species of Molytinae in 86.6% of all examined morphospecies, surpassing a threshold value of 3% GD (73.0%). A total of 28 morphospecies exhibiting significant intraspecific divergences were assigned to multiple MOTUs, respectively, suggesting the presence of cryptic diversity or population divergence. The identification of cryptic species within certain morphological species in this study necessitates further investigation through comprehensive taxonomic practices in the future.

Delimiting species, revealing cryptic diversity, and population divergence in Qinghai-Tibet Plateau weevils through DNA barcoding.

The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.

Morphological and Phylogenetic Analyses Reveal Three New Species of Entomopathogenic Fungi Belonging to Clavicipitaceae (Hypocreales, Ascomycota).

This study aims to report three new species of Conoideocrella and Moelleriella from Yunnan Province, Southwestern China. Species of Conoideocrella and Moelleriella parasitize scale insects (Coccidae and Lecaniidae, Hemiptera) and whiteflies (Aleyrodidae, Hemiptera). Based on the phylogenetic analyses of the three-gene nrLSU, tef-1α, and rpb1, it showed one new record species (Conoideocrella tenuis) and one new species (Conoideocrella fenshuilingensis sp. nov.) in the genus Conoideocrella, and two new species, i.e., Moelleriella longzhuensis sp. nov. and Moelleriella jinuoana sp. nov. in the genus Moelleriella. The three new species were each clustered into separate clades that distinguished themselves from one another. All of them were distinguishable from their allied species based on their morphology. Morphological descriptions, illustrations, and comparisons of the allied taxa of the four species are provided in the present paper. In addition, calculations of intraspecific and interspecific genetic distances were performed for Moelleriella and Conoideocrella.

Assessment of fish diversity in the East China Sea hairtail national aquatic germplasm resources conservation zone using DNA barcoding

Based on the fishery resource survey data from 2019 to 2022, the species composition and taxonomic diversity of fish in the East China Sea hairtail national aquatic germplasm resources conservation zone (ECSHZ) were studied through the analysis of 185 COI sequences. The results showed that the 185 fish samples collected belonged to 105 species, 21 orders, 46 families, and 89 genera in terms of their taxonomic status. There are discrepancies between morphological identification and genetic identification results for four fish species. The intraspecific genetic distance ranged from 0 % to 1.0 %, with an average value of 0.3 %. Meanwhile, the interspecies within genus distance ranged from 5.3 % to 22.7 %, with an average of 14.5 %. The outcomes of the division using Automatic Barcoding Gap Discovery (ABGD) and Bayesian phylogenetics and phylogeography (BPP) were concordant, identifying a total of 105 species groups. ABGD and BPP have shown that there was no overlap between intra-species variation and inter-species variation, supporting the existence of a barcoding gap. The results demonstrate the superiority of DNA barcoding in species identification. A phylogenetic tree was constructed using the maximum likelihood method based on the COI gene, which revealed certain limitations of COI in representing phylogenetic relationships at the genus and higher taxonomic levels. Another phylogenetic tree was constructed using 13 mitochondrial protein-coding genes with more genetic information, allowing for a better study of evolutionary relationships of ECSHZ fish species. The tree supported that Carangidae, Polynemidae, Paralichthyidae, Pleuronectidae, Sphyraenidae, and Cynoglossidae were clustered in an independent clade, with Priacanthidae and Lobotidae separating from Perciformes. This study offers DNA barcodes for ECSHZ fish species, providing crucial data support for conserving fish diversity.

DNA barcoding of common freshwater eleotrids (Gobiiformes: Eleotridae) in the Philippines, with a global comparison and notes on their conservation and management

Eleotrids, also known as gudgeons or sleeper gobies, are found mostly in freshwater and mangrove habitats of tropical and subtropical regions. Some eleotrids exhibit minimal morphological variation at the species level. In this study, DNA barcoding was used to assess the molecular diversity of common freshwater eleotrids in the Philippines in relation to other eleotrid species from other countries with available DNA sequences in public databases. A total of 422 mitochondrial DNA cytochrome c oxidase I (COI) gene sequences were analyzed: 107 of which were generated from this study, while the remaining 315 sequences were mined from Barcode of Life Data System and GenBank. Both the neighbor-joining and maximum likelihood trees constructed based on the COI sequences clustered most of the species in concordance with their taxonomic classification. The mean Kimura 2-parameter genetic distances within species and genera were 1.31% and 11.60%, respectively. As expected, the mean interspecific distance was higher than the mean intraspecific distance except in some species. This study revealed the presence of nine distinct eleotrid species belonging to five genera in the Philippines. These species include Giuris laglaizei, G. tolsoni, Eleotris acanthopomus, E. fusca, E. melanosoma, Belobranchus sp., Belobranchus belobranchus, Butis butis, and Ophiocara ophicephalus. This study also revealed the presence of possibly undescribed Belobranchus species in the Philippines. This undescribed Belobranchus species differs by a high percentage of genetic divergence from the other species of Belobranchus (3.00% from B. segura and 13.40% from B. belobranchus). Furthermore, high genetic distance (2.62%) was also observed between G. laglaizei species of Laguna de Bay and Mindanao. This study strongly recommends a taxonomic review of the Laguna de Bay G. laglaizei and the Philippine Belobranchus spp., as these species may harbor species complexes that require closer examination so that proper conservation and management measures can be implemented for each species.

Two new species of Platynothrus and Heminothrus (Oribatida: Crotoniidae) from Mexico

The oribatid mite genera Platynothrus and Heminothrus currently comprise 20 and 10 species, respectively, and collectively have a cosmopolitan distribution. They have been classified into three to five subgenera, depending on the classification. For Platynothrus, a couple of new species have been described in the last two years, while for Heminothrus, the last formal description of a new species was 26 years ago. In this study, we describe two new species of these crotoniid mites, discovered in the soil and litter of a tropical montane cloud forest in Mexico. One of these new species belongs to the genus Platynothrus, which can be distinguished from other species of this genus by the short clavate sensillus, curved smooth interlamellar seta, and the length of the notogastral setae. The second new species belongs to the genus Heminothrus, being characterized by a short rhomboidal sensillus and a very long interlamellar seta. Intraspecific genetic distances of the COX-1 mitochondrial marker were 2.15%, and 0.81% for the new Platynothrus and Heminothrus species, respectively.

Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach.

Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes. In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae. In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.

When standard DNA barcodes do not work for species identification: intermixed mitochondrial haplotypes in the Jaera albifrons complex (Crustacea: Isopoda)

Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species.

Phylogeography of a Widely Distributed Atlantic Species: The Case of the Ghost Crab Ocypode quadrata (Fabricius, 1787) (Decapoda: Brachyura: Ocypodidae)

Ocypode Weber, 1795 (Brachyura: Ocypodidae) is popularly known as ghost crab, and encompasses 21 valid species, including Ocypode quadrata (Fabricius, 1787). This species has wide distribution along the Atlantic coast of America, from the USA (Massachusetts) to Brazil (Rio Grande do Sul), Central America, and Antilles. Such distribution, along with some biological characteristics of its life cycle and the presence of geographic barriers, could lead to genetic structuring. Herein, we evaluate the hypothesis of the presence of geographic barriers using COI and 16S partial gene fragments. The Maximum Likelihood tree suggests the monophyly of O. quadrata, while the values of intraspecific genetic distance along with the star-shaped haplotype network suggested a lack of genetic structure in Brazilian, Panama, and French Guiana populations, probably caused by larval dispersion. USA and Mexico populations may be a new lineage, but we cannot say it with few sequences and with no morphological characters.

Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding.

The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.