Phylogeography of cliff racer (Platyceps rhodorachis Jan, 1865) from Punjab, Pakistan

The present study reports the existence of cliff racer, Platyceps rhodorachis from the plains of Punjab, Pakistan. A total of 10 specimens were captured during the field surveys from June to September, 2018 from different sites of Punjab. Platyceps rhodorachis was identify on the basis of morphology and confirmed through COI gene sequences. The obtained DNA sequences have shown reliable and exact species identification. Newly produced DNA sequences of Platyceps rhodorachis were submitted to GenBank and accession numbers were obtained (MK936174.1, MK941839.1 and MT790210.1). N-J tree based on COI sequences of Platyceps rhodorachis clearly separated as out-group with other members of family Colubridae based on p-distance. The intra-specific genetic variation ranges from 12% to 18%. The DNA sequences of Platyceps rhodorachis kashmirensis, Platyceps rhodorachis ladacensis, Platyceps ventromaculatus, Platyceps ventromaculatus bengalensis and Platyceps ventromaculatus indusai are not available at NCBI to validate their taxonomic positions. In our recommendations, a large scale molecular based identification of Pakistan’s herpetofauna is required to report more new or subspecies from country.

Thelytokous Reproduction of Onion Thrips, Thrips tabaci Lindeman 1889, Infesting Welsh Onion and Genetic Variation among Their Subpopulations

Parthenogenesis is not uncommon in thrips. This asexual reproduction produces males (arrhenotokous) or female (thelytokous). Only females are found in the onion thrips (Thrips tabaci Lindeman 1889) infesting Welsh onion (Allium fistulosum) in several areas of Korea. To determine the reproduction mode of T. tabaci, thrips infesting Welsh onion were collected from different localities in Korea. Cytochrome oxidase I (COI) sequences were then assessed. Results showed that all test local populations had signature motif specific to a thelytokous type. These COI sequences were clustered with other thelytokous populations separated from arrhenotokous T. tabaci populations. In a laboratory test, individual rearing produced female progeny without any males. These results support that Korean onion thrips infesting Welsh onion have the thelytokous type of parthenogenesis. Local thrips populations exhibited significant variations in susceptibility to chemical and biological insecticides. Random amplified polymorphic DNA (RAPD) analysis indicated genetic variations of local populations. However, the genetic distance estimated from RAPD was independent of the actual distance among different local populations. These results suggest that genetic variations of T. tabaci are arisen from population subdivision due to asexual thelytokous reproductive mode.

Genetic variability and population structure of Leucinodes orbonalis (Guenée), a severe insect pest of brinjal in India

Aim: The present study was undertaken to provide valuable insights regarding population genetic structure of Leucinodes orbonalis from diverse agro-ecologies of India. Methodology: Molecular characterization of L. orbonalis populations collected from five major agro-climatic zones of India was carried out using mitochondrial cytochrome oxidase I (COI) gene. Collected specimens were subjected to DNA extractions, partial PCR amplification and sequencing of the target gene, and multiple sequence alignments. Results: The results showed very less diversity in the nucleotide positions of the COI sequences of 79 studied specimens, with a low number of segregating sites (30), nucleotide diversity (0.00438) and overall mean genetic distance (0.004 ± 0.001). The significant negative values of neutrality tests and unimodal mismatch distribution supported the demographic expansion theory in Indian L. orbonalis. Analysis of the molecular variance revealed that 93.13% of the genetic variation was within populations, and the variation among populations was only 6.87%. The pairwise genetic differentiation was also found to be low to moderate between most of the populations. Multiple haplotypes were recorded from all the populations, and both neighbour-joining tree as well as the haplotype network showed that clustering of the haplotypes was independent of the geographical location. Interpretation: Thus, it can be inferred that Indian populations of L. orbonalis have very low genetic variation levels concerning the COI gene. There is a possible occurrence of stable inherited gene flow among populations, thereby reducing genetic variation in India.

Molecular Identification and Appraisal of the Genetic Variation of Taenia saginata in Central Regions of Vietnam

Taenia saginata is a globally distributed tapeworm responsible for human taeniasis due to the ingestion of raw or undercooked beef. T. saginata is present in several Asian countries, including China, Thailand, Lao PDR, Cambodia, and Vietnam, but little is known about its genetic variation. Studying the tapeworm’s phylogeographic patterns is crucial to better understanding their association with the geographic distribution of taeniasis/cysticercosis in human populations. In the present study, 38 specimens of this putative species were collected in central regions of Vietnam and analysed using the mitochondrial gene Cytochrome c Oxidase subunit I (COI) as a molecular marker to assess the correct species identification and investigate the level of genetic variation at different geographic scales. Phylogenetic and phylogeographic analyses were carried out on a dataset that included COI sequences from Vietnamese specimens and from all conspecifics available in GenBank to date. The results showed that the collected Vietnamese specimens belonged to the species T. saginata. In Southeast Asia, signs of a possible founder effect were discovered, with the most common haplotypes frequent and present in many countries, except Lao PDR, which shares its most common haplotype only with individuals from Thailand. Remarkably, a unique taxonomic entity was found worldwide, even though the available COI sequences of T. saginata belonging to non-Asiatic countries are, at present, limited. Therefore, future studies including more COI sequences from a higher number of countries and the use of a combined molecular approach with multiple genetic markers would be useful to provide deeper insight into the global genetic variation of this species.

New records of the occurrence of Megaleporinus macrocephalus () (Characiformes, Anostomidae) from the basins of the Itapecuru and Mearim rivers in Maranhão, Northeastern Brazil

The “piaussu”, Megaleporinus macrocephalus is an anostomatid fish species native to the basin of the Paraguay River, in the Pantanal biome of western Brazil. However, this species has now been recorded in a number of other drainages, including those of the upper Paraná, Uruguay, Jacuí, Doce, Mucuri, and Paraíba do Sulrivers. This study presents two new records of the occurrence of M. macrocephalus, in the basins of the Itapecuru and Mearim rivers in the state of Maranhão, in the Brazilian Northeast. The piaussu is a large-bodied fish of commercial interest that is widely raised on fish farms, and its occurrence in the Itapecuru and Mearim rivers is likely the result of individuals escaping from fish tanks when they overflow during the rainy season. Morphological analyses and sequences of the Cytochrome Oxidase Subunit I (COI) gene confirmed the taxonomic identification of the specimens as M. macrocephalus. The COI sequences were 99.66% similar to those of M. macrocephalus deposited in the BOLDSystems database. These records extend the known distribution of M. macrocephalus to the basins of the Itapecuru and Mearim rivers in the Brazilian Northeast, highlighting a new case of introduction of exotic fish species into Brazilian river basins.

Three new species of Byrsopteryx Flint microcaddisflies from Peru (Insecta: Trichoptera) including DNA-based larval associations

In this paper, we have described and illustrated three new species of Byrsopteryx from Peru: Byrsopteryx inti, sp. nov. Byrsopteryx mamaocllo sp. nov., and Byrsopteryx mancocapac sp. nov. Larvae of the latter two were also associated to male specimens based on comparison of a fragment of COI gene and pharate male identification. Byrsopteryx inti sp. nov. and Byrsopteryx mamaocllo sp. nov. share a unique feature: a semi-dome process formed by a thickened area on male forewings. The three species can be easily identified by wing coloration and male genitalia. Furthermore, Byrsopteryx inti sp. nov. can be recognized by its sternum VIII with a median digitate process on posterior margin, slightly capitate; and by long dorsolateral processes from segment VIII, which cross each other apically in dorsal view. Byrsopteryx mamaocllo sp. nov. can be distinguished by sternum VIII bearing a pair of short, posterior, spinelike processes, which are curved inwards and bordered by a rounded, membranous structure, and by a pair of short, heavily sclerotized, dorsolateral processes. Byrsopteryx mancocapac sp. nov. can be distinguished by strong spine-like processes arising dorsally from subgenital plate and by sternum VIII with posterior margin divided into two plate-like lobes. Larvae of B. mamaocllo sp. nov. and B. mancocapac sp. nov. are similar to other Byrsopteryx larvae known. They can be distinguished from each other by the shape of the operculum formed by terga VIII and IX, and number of setae on the second abdominal pleurite. Maximum likelihood analyses of 20 COI sequences, including nine Byrsopteryx species, placed B. inti sp. nov. and B. mamaocllo sp. nov. as sister species and related to a clade including B. gomezi, B. tapanti, and B. esparta, while B. mancocapac sp. nov. was found as sister to B. abrelata. Despite the close phylogenetic relationship found between B. inti sp. nov. and B. mamaocllo sp. nov., they are separated by 14.9% minimum K2P divergence of COI. The highest intraspecific distance observed was 1.4% for B. mancocapac sp. nov. individuals. Although the Peruvian caddisfly fauna has around 320 known species and almost a third of them are microcaddisflies, in this paper we present the first descriptions of Byrsopteryx species for the country.

High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)

Accurate identification and association of larval specimens with adults is a major challenge in insect taxonomy. Fortunately, it is now possible for nonexperts to sort collections of bulk samples with DNA barcodes rapidly and cost-effectively. We demonstrate this process using nanopore barcoding of 757 marine insects (Insecta: Gerromorpha), of which 81% were nymphs and many samples did not have co-occurring adult males for specific identification. We successfully associated 738 specimens (97%) to nine gerromorphan species, which would have been impossible to identify using morphological characters alone. This improved ability to incorporate information from all life-history stages has led to greater precision of species distributional ranges—knowledge that will be crucial for a more complete understanding of marine insects. We also highlighted two distinct, nonoverlapping Gerromorpha COI sequence databases on GenBank—a consequence of using two different primer sets to amplify different regions of COI. This issue inevitably hinders species identification with DNA-based methods, particularly for poorly represented groups such as marine insects. We bridged these databases by analyzing full-length COI sequences. We believe this will inspire future studies to incorporate DNA-based methods for more adult–larval association studies and for enhancing existing genetic resources, especially in understudied groups.

New records of water mites from the Balkans revealed by DNA barcoding (Acari, Hydrachnidia)

New records of water mites from Serbia, North Macedonia and Greece revealed by DNA barcoding are presented. DNA barcodes were recovered from 63 water mite specimens morphologically assigned to 32 species. One species Lebertia algeriensis Lundblad, 1942, is reported for the first time for the Balkans; four species, i.e. Lebertia fimbriata Thor, 1899, L. rivulorum K. Viets, 1933, Atractides stankovici Pešić & Gerecke, 2010, and Wettina lacustris Pešić & Smit, 2018 are new for North Macedonia; Monatractides madritensis (K. Viets, 1930) and Mideopsis roztoczensis Biesiadka & Kowalik, 1979 are new for Serbia; and Hygrobates mediterraneus Pešić, 2020 is new for Greece. Comparing sequences of our study with the available COI sequences we recognized five possible cases of cryptic diversity involving species clusters with more than 5% divergence indicating that these species need further study.

New records of leeches of the genus Limnatis (Hirudinea, Praobdellidae) from the South Caucasus and Central Asia: phylogenetic relationships of Eurasian and African populations

Leeches of the genus Limnatis Moquin–Tandon, 1827 infest mucous membranes of various mammals, including humans and domestic ungulates. The type species of the genus L. nilotica (Savigny, 1822) was initially thought to occur throughout the Western Palaearctic, from North Africa to the Middle East and Central Asia. It was later found that L. paluda (Tennent, 1859) is a widespread Western Asian species. However, the South Caucasus and vast areas of Central Asia have not been explored sufficiently in terms of leeches of the genus Limnatis. We recorded L. paluda from Azerbaijan and Uzbekistan for the first time. We also carried out the first molecular characterisation of L. nilotica herein. We found a deep genetic differentiation (8 %) between the Western Asian L. paluda and North African (Moroccan) L. nilotica based on their COI sequences. This finding corroborates a previous morphology–based hypothesis on their separate species assignments. The low genetic diversity of L. paluda is explained by the recent colonisation of arid landscapes of Western Asia.

Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences

[Definitive version of this article may be found here] The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI ‘barcoding’ primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata. The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar lobates (Lampocteis sp. ‘V’ stratified by depth, and ‘A’ differentiated by color). The newly described primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyze environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.