Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

First record of Telenomus fariai Costa Lima, 1927 (Hymenoptera, Scelionidae, Telenominae) as a parasitoid of Triatoma dimidiata (Latreille, 1811) (Hemiptera, Reduviidae, Triatominae) eggs in Mexico

The egg parasitoid Telenomus fariai Costa Lima (Hymenoptera, Scelionidae), is reported for the first time in Veracruz, Mexico. Telenomus fariai was discovered in 2019 during a field collection of Triatoma dimidiata L. (Hemiptera, Reduviidae), representing the first report of its association with Tr. dimidiata in Mexico. This species is here redescribed and sequencing of a portion of the cytochrome oxidase 1 gene (COI) was performed to facilitate future identifications and to examine host associations between species of Telenomus Haliday and Reduviidae in a broader context.

Rhyacophila siparantum sp. nov. (Trichoptera: Rhyacophilidae), a new species of the R. philopotamoides species group from the Republic of Kosovo with molecular and ecological notes

In this study we describe Rhyacophila siparantum sp. nov., a new species of the Rhyacophila philopotamoides species group from the Bjeshkët e Nemuna Mountains in Kosovo, based on morphological (male adults) and molecular (sequencing of the barcode region of the cytochrome c oxidase subunit I gene (COI)) characteristics. The new species is morphologically closest to Rhyacophila schmidinarica Urbanič, Krušnik & Malicky, 2000, and also closely resembling Rhyacophila hirticornis McLachlan, 1879. R. siparantum sp. nov. differs from both its most similar congeners primarily by the shape of the segment X, which is in lateral view short apically and with a pronounced lateral hump on the posterior edge. This difference, combined with other characters related to the shape of the second segment of inferior appendages, spine pattern of parameres and size of ventral teeth on segments VI and VII, make R. siparantum sp. nov. easily distinguishable from both most similar congeners. Phylogenetic and taxonomic relationships were reconstructed using two methods of phylogenetic inference, and two species delimitation methods. All this supports Rhyacophila siparantum sp. nov. as a distinct taxon. The adults of Rhyacophila siparantum sp. nov. were found during the period May – August, nearby a small rheocrene spring inside a forested area. The new species is most probably a microendemic of the Bjeshkët e Nemuna, a mountainous massive known for several other endemic species of caddisflies. Rhyacophila siparantum sp. nov. is the seventeenth known species of the genus Rhyacophila Pictet, 1834 from Kosovo.

Every Single Specimen Counts: A New Docosia Winnertz (Diptera: Mycetophilidae) Species Described from a Singleton

A new species—Docosia caucasica sp. n.—has been described from material collected from the Lesser Caucasus Mountains in Georgia (Sakartvelo). The new species belongs to a group of Palaearctic species characterized by distinct posterolateral processes of gonocoxites and apically modified setae at the posteroventral margin of the gonocoxites medially. Within the group, D. caucasica sp. n. is most similar to D. landrocki Laštovka and Ševčík, 2006 in having a similar outline of the medial process of posteroventral margin of the gonocoxites and the gonostylus. There is also a marked difference within the partial cytochrome c oxidase subunit 1 gene (COI) sequence of D. caucasica sp. n. and other Docosia spp. available in public databases. As the new species is described from a single male specimen only, the adequacy and code compliance of that are discussed.

Evolution of New Zealand's Marine Caddisflies: A Phylogenetic and Phylogeographic Assessment of the Chathamiidae (Insecta: Trichoptera)

<p><b>The Chathamiidae are an interesting family of caddisflies, unusual as all of the five known species are believed to breed entirely within the marine intertidal, comprising one of very few known marine insect groups. Additionally the family approaches almost complete endemicity status in New Zealand, and may represent an ancient lineage representative of ancient vicariance from Gondwana. However one species, the common and widespread Philanisus plebeius is also known to have a disjunct population in New South Wales Australia, hypothesised to represent a recent anthropogenic dispersal. This thesis, using DNA information, examined the Chathamiidae at varying phylogenetic levels.</b></p> <p>Firstly the species Philanisus plebeius was incorporated into a thorough intraspecific phylogeography, including samples from both New Zealand and Australia. The population as a whole was genetically diverse, with the population divisible into two major haplogroups, each restricted to discrete geographic areas with no overlap being observed. One of these groups was restricted to just two localities in the central eastern North Island, whereas the remainder included most remaining samples from both Islands of New Zealand, and also Australia. All Australian samples were found to comprise a single haplotype, differing by a single base pair from the most common haplotype in New Zealand. It was decided that the Australian population therefore represents a recent dispersal event from New Zealand, although unless the Australian haplotype remains undiscovered in New Zealand the level of divergence found is not congruent with a human introduction. One sequence intermediate between the two major haplogroups was identified from a single haplotype from Tauranga. It seemed that much of the population of Philanisus plebeius has been affected by recent demographic expansion, likely due to the effects of the last glacial maximum (LGM).</p> <p>The five species of the Chathamiidae were then analysed in a phylogeny. It was found that the genus Chathamia was polyphyletic, with the species C. integripennis nested within the genus Philanisus. The remaining species, C. brevipennis from the Chatham Islands, was basal to all the remaining members of the family. A strict molecular clock found a recent Pleistocene age (roughly 0.5 Ma) for divergence of the Kermadec Island species Philanisus fasciatus, and a Pliocene-Pleistocene age (roughly 3 Ma) for the Chatham Island species Chathamia brevipennis. For a comparison with the species C. brevipennis, the other Chatham Island caddisfly taxa Oecetis chathamensis, and Hydrobiosis lindsayi were compared with New Zealand relatives; indicated to have late and early Pleistocene ages respectively. A short sequence of the gene COI was amplified for the species Philanisus mataua, however this was found to contain two sequences reflecting either heteroplasmy or sample contamination, inhibiting confident phylogenetic placement. Additionally a larval sample from Sydney was demonstrated to represent C. integripennis, recorded outside of Northern New Zealand for the first time. Finally the Chathamiidae was included in a higher level phylogeny with related families, and was show to comprise a monophyletic group, sister to the Australasian family of the Conoesucidae. A relaxed molecular clock estimated a Cretaceous (roughly 90 Ma) age for the Chathamiidae, congruent with a vicariant age in New Zealand.</p>

Evolution of New Zealand's Marine Caddisflies: A Phylogenetic and Phylogeographic Assessment of the Chathamiidae (Insecta: Trichoptera)

<p><b>The Chathamiidae are an interesting family of caddisflies, unusual as all of the five known species are believed to breed entirely within the marine intertidal, comprising one of very few known marine insect groups. Additionally the family approaches almost complete endemicity status in New Zealand, and may represent an ancient lineage representative of ancient vicariance from Gondwana. However one species, the common and widespread Philanisus plebeius is also known to have a disjunct population in New South Wales Australia, hypothesised to represent a recent anthropogenic dispersal. This thesis, using DNA information, examined the Chathamiidae at varying phylogenetic levels.</b></p> <p>Firstly the species Philanisus plebeius was incorporated into a thorough intraspecific phylogeography, including samples from both New Zealand and Australia. The population as a whole was genetically diverse, with the population divisible into two major haplogroups, each restricted to discrete geographic areas with no overlap being observed. One of these groups was restricted to just two localities in the central eastern North Island, whereas the remainder included most remaining samples from both Islands of New Zealand, and also Australia. All Australian samples were found to comprise a single haplotype, differing by a single base pair from the most common haplotype in New Zealand. It was decided that the Australian population therefore represents a recent dispersal event from New Zealand, although unless the Australian haplotype remains undiscovered in New Zealand the level of divergence found is not congruent with a human introduction. One sequence intermediate between the two major haplogroups was identified from a single haplotype from Tauranga. It seemed that much of the population of Philanisus plebeius has been affected by recent demographic expansion, likely due to the effects of the last glacial maximum (LGM).</p> <p>The five species of the Chathamiidae were then analysed in a phylogeny. It was found that the genus Chathamia was polyphyletic, with the species C. integripennis nested within the genus Philanisus. The remaining species, C. brevipennis from the Chatham Islands, was basal to all the remaining members of the family. A strict molecular clock found a recent Pleistocene age (roughly 0.5 Ma) for divergence of the Kermadec Island species Philanisus fasciatus, and a Pliocene-Pleistocene age (roughly 3 Ma) for the Chatham Island species Chathamia brevipennis. For a comparison with the species C. brevipennis, the other Chatham Island caddisfly taxa Oecetis chathamensis, and Hydrobiosis lindsayi were compared with New Zealand relatives; indicated to have late and early Pleistocene ages respectively. A short sequence of the gene COI was amplified for the species Philanisus mataua, however this was found to contain two sequences reflecting either heteroplasmy or sample contamination, inhibiting confident phylogenetic placement. Additionally a larval sample from Sydney was demonstrated to represent C. integripennis, recorded outside of Northern New Zealand for the first time. Finally the Chathamiidae was included in a higher level phylogeny with related families, and was show to comprise a monophyletic group, sister to the Australasian family of the Conoesucidae. A relaxed molecular clock estimated a Cretaceous (roughly 90 Ma) age for the Chathamiidae, congruent with a vicariant age in New Zealand.</p>

Diversity of Three Small Type’s Giant Clams and Their Associated Endosymbiotic Symbiodiniaceae at Hainan and Xisha Islands, South China Sea

Giant clams are found in a mutualistic association with Symbiodiniaceae dinoflagellates, however, the diversity of the giant clams, as well as the diversity and distribution of Symbiodiniaceae in different Tridacnine species remain relatively poorly studied in the South China Sea. In this study, a total of 100 giant clams belonging to small type’s giant clams, Tridacna maxima, T. crocea, and T. noae, were collected from Hainan and Xisha Islands. Based on mtDNA cytochrome c oxidase subunit 1 gene (COI) and 16S rRNA fragments, T. maxima and T. crocea showed a closer phylogenetic relationship than T. noae. All the three species of giant clams hosted Symbiodiniaceae including genera Symbiodinium (formerly Clade A) and Cladocopium (formerly Clade C). Geographically, symbionts in Cladocopium are restricted to Xisha Islands, probably because Cladocopium prefers to inhabit in waters with higher mean temperatures. The endosymbiont specificity among the three giant clam species was also detected. T. noae and T. crocea are found to harbor Symbiodinium preferentially, compared with Cladocopium. These results could provide important information to understand various endosymbionts occurring in giant clams in the South China Sea.

Bacteria are everywhere, even in your COI marker gene data!

The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in eDNA metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units or/and amplicon sequence variants are retrieved from such studies and referred to as "dark matter", and do not get a taxonomic assignment with a reference sequence. For a thorough investigation of this dark matter, we have developed the Dark mAtteR iNvestigator (DARN) software tool. A reference COI-oriented phylogenetic tree was built from 1,240 consensus sequences covering all the three domains of life, with more than 80% of those representing eukaryotic taxa. With respect to eukaryotes, consensus sequences at the family level were constructed from 183,330 retrieved from the Midori reference 2 database. Similarly, sequences from 559 bacterial genera and 41 archaeal were retrieved from the BOLD database. DARN makes use of the phylogenetic tree to investigate and quantify pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of phylogenetic assignments. To evaluate DARN, both environmental and bulk metabarcoding samples from different aquatic environments using various primer sets were analysed. We demonstrate that a large proportion of non-target prokaryotic organisms such as bacteria and archaea are also amplified in eDNA samples and we suggest bacterial COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter. DARN source code is available on GitHub at https://github.com/hariszaf/darn and you may find it as a Docker at https://hub.docker.com/r/hariszaf/darn.

CALLIPHORIDAE (REVIEW)

The Calliphoridae family attracts many researchers in the phylogeny of myiasis in this family. Nevertheless, even after more than 50 years of research of the phylogenetic relationships among Calliphoridae subfamilies, the origin of myiasis remains unclear. By studying the peculiarities of the ecology of blue-green meat flies, and their adaptation to various habitats, it was found that the transition to facultative parasitism at the larval stage could occur in several ways, and was accompanied by the formation of viviparity. The larval parasitism of Calliphoridae on birds developed as a tendency of evolution. Larvae of the genus Protocalliphora, began feeding on blood of birds, and larvae of the species of the genus Trypocalliphora feed on the host tissues causing myiasis and the death of chicks. In order to elucidate the problem, we constructed three phylogenetic trees using nucleotide sequence data from cytochrome oxidase subunit one gene (COI), representing a mitochondrial conservative gene, and nuclear 28S subunit of ribosomal RNA gene (28S rRNA) in order to interpret the evolutionary profile of myiasis in the family Calliphoridae. Comparative analysis of the phylogenetic trees shows that the habit of obligatory myiasis originated independently more than five times among different calliphorid taxa in the course of evolutionary history. The inclusion of other myiasis-causing families (Oestridae, Gastrophilidae, and Sarcophagidae) along with fundamental life-history studies that deal with biology, physiology, feeding behavior and host specificity in addition to phylogenetic analysis could provide a more accurate answer to the origin of myiasis

The Role of Mitochondria in Carcinogenesis

The mitochondria are essential for normal cell functioning. Changes in mitochondrial DNA (mtDNA) may affect the occurrence of some chronic diseases and cancer. This process is complex and not entirely understood. The assignment to a particular mitochondrial haplogroup may be a factor that either contributes to cancer development or reduces its likelihood. Mutations in mtDNA occurring via an increase in reactive oxygen species may favour the occurrence of further changes both in mitochondrial and nuclear DNA. Mitochondrial DNA mutations in postmitotic cells are not inherited, but may play a role both in initiation and progression of cancer. One of the first discovered polymorphisms associated with cancer was in the gene NADH-ubiquinone oxidoreductase chain 3 (mt-ND3) and it was typical of haplogroup N. In prostate cancer, these mutations and polymorphisms involve a gene encoding subunit I of respiratory complex IV cytochrome c oxidase subunit 1 gene (COI). At present, a growing number of studies also address the impact of mtDNA polymorphisms on prognosis in cancer patients. Some of the mitochondrial DNA polymorphisms occur in both chronic disease and cancer, for instance polymorphism G5913A characteristic of prostate cancer and hypertension.