On two new species of deep-sea carrier crabs (Crustacea, Brachyura, Homolodromiidae, Dicranodromia) from Taiwan and the Philippines, with notes on other Indo-West Pacific species

The systematics of four species of the homolodromiid genus Dicranodromia A. Milne-Edwards, 1880, from East Asia and the Philippines is reappraised: D. danielae Ng & McLay, 2005, D. doederleini Ortmann, 1892, D. karubar Guinot, 1993, and D. martini Guinot, 1995; and key characters such as the epistome, gonopods, and spermatheca are figured in detail. Two new species, D. erinaceussp. nov. and D. robustasp. nov., are described from Taiwan and the Philippines, respectively. Dicranodromia erinaceussp. nov. resembles D. spinulata Guinot, 1995, and D. delli Ahyong, 2008 (from New Caledonia and New Zealand) but can be separated by its distinctly spinulated carapace surfaces and proportionately shorter fifth ambulatory legs. Dicranodromia robustasp. nov. is superficially similar to D. baffini (Alcock & Anderson, 1899) and D. karubar Guinot, 1993, but can easily be separated by possessing a broad dorsoventrally flattened infraorbital tooth. A genetic study of the species using the mitochondrial cytochrome c oxidase I gene confirms that the taxa are distinct, with D. erinaceussp. nov. coming out in a well-supported clade from congeners. The megalopa of D. doederleini is also reported for the first time.

Vector-Borne Pathogens in Ticks and Fleas of Client-Owned Dogs in Metro Manila, Philippines

Rhipicephalus sanguineus s.l. and Ctenocephalides felis are considered the most prevalent ectoparasites of dogs in the Philippines. Vector-borne pathogens (VBPs) in these ectoparasites pose health risks to humans and animals. This study aimed to confirm the morphological and molecular identity of tick and flea species parasitising dogs in Metro Manila (Philippines) and molecularly investigate the possible presence of Bartonella spp., Rickettsia spp., Ehrlichia canis, and Anaplasma platys DNA. Ticks (n = 58) and fleas (n = 52) on dogs from three veterinary clinics in Metro Manila were collected and identified morphologically and molecularly via amplification and sequencing of cytochrome c oxidase I (cox1). Aliquots of ectoparasite DNA underwent real-time polymerase chain reaction (qPCR) screening for VBPs. All ticks were R. linnaei (formerly R. sanguineus s.l. “tropical lineage”), while all fleas were C. felis from clade 6 of the tropical II cluster/“Cairns” clade known from Australia. DNA of B. clarridgeiae was detected in 10% of fleas. DNA of R. felis was detected in 10% of fleas and in 3.8% of ticks. DNA of E. canis and A. platys was not detected. This study confirmed the presence of ticks and fleas as frequent ectoparasites on dogs and VBP presence emphasises the importance of preventative actions for animal health and welfare.

Occurrence and molecular identification of an invasive rice strain of fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Sindh, Pakistan, using mitochondrial cytochrome c oxidase I gene sequences

The fall armyworm (FAW), an invasive pest of maize, is an emerging threat in Southern Asia after America and Europe. Recently, this notorious pest has also been found in different areas of Pakistan. To assess its presence in Pakistan, a survey was carried out in the provinces of Punjab, Sindh, and Khyber Pakhtunkhwa during May–October 2019. We observed the highest incidence of FAW in Sindh with maximum impact in districts Tando-Allahyar and Hyderabad. These samples were identified as Spodoptera frugiperda on the morphological and taxonomical bases. However, morphological identification of this pest is very difficult at early larval instars. Here, we use the mitochondrial cytochrome c oxidase I (COI) gene region for the precise identification of larva of this invasive pest at species level. Two different regions of COI gene (COI-5′ and COI-3′) were used as molecular markers for the identification of this species. DNA sequence similarity searches of the obtained COI gene sequences (NCBI GenBank Accession Nos. MW241537, MW241538, MW349515, MW349516, MW349493 and MW349494) revealed that genetically it is more than 99% identical to S. frugiperda. The phylogenetic analysis indicated it as the rice-strain (R-strain). Both 3′- and 5′-fragment tree topologies showed that the collected samples of the FAW species belong to the R-strain. To the best of our knowledge, this is the first report providing molecular evidence for the existence of R-strain of S. frugiperda that was found feeding on maize crop in Sindh, Pakistan, using COI gene sequences as a marker.

Do pseudogenes pose a problem for metabarcoding marine animal communities?

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. The number of NUMTs meeting four length criteria (>150 bp, >300 bp, >450 bp, >600 bp) was determined, and they were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 389 NUMTs <100 bp were detected, with an average of 2.49 per species (range = 0–50) and a mean length of 336 bp +/- 208 bp. Among NUMTs lacking diagnostic features, 52.5% were ≤300 bp, 63.9% were ≤450 bp, and 76.2% were ≤600 bp. Studies examing 150 bp amplicons inflate the OTU count by 1.57x compared to the true species count and increase perceived intraspecific variation at COI by 1.19x (when sequence variants with >2% sequence divergence are recognized as different OTUs). There was a weak positive correlation between genome size and NUMT count but no variation among phyla, trophic groups or life history traits. While bioinformatic advances will improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.

Illegal, Unreported, and Unregulated Fisheries Threatening Shark Conservation in African Waters Revealed from High Levels of Shark Mislabelling in Ghana

Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, contributing to overexploit substitute species that are undetectable when sold under wrong names. This is the first study of DNA barcoding to assess the level of mislabelling in fish marketed in Ghana, focusing on endangered shark species. Genetic identification was obtained from 650 base pair sequences within the cytochrome c oxidase I (COI) gene. All except one of 17 shark fillets analysed were wrongly labelled as compared with none of 28 samples of small commercial pelagic fish and 14 commercial shark samples purchased in Europe. Several substitute shark species in Ghana are endangered (Carcharhinus signatus and Isurus oxyrinchus) and critically endangered (Squatina aculeata). Shark products commercialized in Europe (n = 14) did not reveal mislabelling, thus specific shark mislabelling cannot be generalized. Although based on a limited number of samples and fish markets, the results that reveal trade of endangered sharks in Ghana markets encourage Ghanaian authorities to improve controls to enforce conservation measures.

DNA barcoding pada invertebrata laut

Banyaknya spesies invertebrata laut yang memiliki kemiripan morfologi menyebabkan kesalahan identifikasi sangat mungkin terjadi. Identifikasi spesies secara molekuler sangat diperlukan dalam mempelajari taksonomi yang akurat. Penelitian ini bertujuan untuk menentukan identitas invertebrata laut dari Perairan Papua dengan teknik DNA barcoding menggunakan marka gen COI (Cytochrome c oxidase I). Penelitian mengidentifikasi 29 individu invertebrata laut, yang terdiri dari teripang (6 sampel), lobster (6 sampel), gurita (6 sampel), chiton (5 sampel), dan bulu babi (6 sampel). Metode identifikasi molekuler terdiri dari isolasi DNA, PCR fragmen gen COI, sekuensing, dan analisis sekuens DNA menggunakan software bioinformatika.Hasil penelitian ini menunjukkan bahwa teripang merupakan spesies Bohadschia marmorata, lobser merupakan spesies Panulirus versicolor, gurita merupakan spesies Octopus cyanea, chiton merupakan spesies Ischnochiton australis, dan bulu babi merupakan spesies Tripneustes gratilla, berdasarkan analisis BLAST dan Boldsystem. Dengan tingkat kemiripan sampel dan rujukan dalam kisaran 84.58 sampai 100.00%. Indeks disparitas, jarak genetik dan pohon filogenetik mendukung hasil ini.

Updating the bionomy and geographical distribution of Anopheles (Nyssorhynchus) albitarsis F: A vector of malaria parasites in northern South America

Anopheles albitarsis F is a putative species belonging to the Albitarsis Complex, recognized by rDNA, mtDNA, partial white gene, and microsatellites sequences. It has been reported from the island of Trinidad, Venezuela and Colombia, and incriminated as a vector of malaria parasites in the latter. This study examined mitochondrially encoded cytochrome c oxidase I (MT-CO1) sequences of An. albitarsis F from malaria-endemic areas in Colombia and Venezuela to understand its relations with other members of the Complex, revised and update the geographical distribution and bionomics of An. albitarsis F and explore hypotheses to explain its phylogenetic relationships and geographical expansion. Forty-five MT-CO1 sequences obtained in this study were analyzed to estimate genetic diversity and possible evolutionary relationships. Sequences generated 37 haplotypes clustered in a group where the genetic divergence of Venezuelan populations did not exceed 1.6% with respect to Colombian samples. Anopheles albitarsis F (π = 0.013) represented the most recent cluster located closer to An. albitarsis I (π = 0.009). Barcode gap was detected according to Albitarsis Complex lineages previously reported (threshold 0.014–0.021). Anopheles albitarsis F has a wide distribution in northern South America and might play an important role in the transmission dynamics of malaria due to its high expansion capacity. Future studies are required to establish the southern distribution of An. albitarsis F in Venezuela, and its occurrence in Guyana and Ecuador.

Taxonomy of Centropomus Lacépède, 1802 (Perciformes: Centropomidae), with focus on the Atlantic species of the genus

Centropomus Lacépède, 1802 comprises 13 species of the fishes popularly knows as snooks, distributed in both Atlantic and Pacific coasts of America. Despite several studies on the group, conflicting taxonomic classifications still exist, including overlapping diagnostic characters, rendering species diagnoses extremely difficult. Herein, we review the taxonomy of Centropomus to elucidate species identities, redefine their diagnoses and to assess interspecific relationships based on the examination of 376 specimens. The study included complementary approaches, as analyses of external morphologic characters, linear and geometric morphometrics, and molecular analyses. Forty-nine characters were used for external morphology, 17 discrete plus 32 linear measurements. Shape and size were analyzed through geometric morphometrics of 185 specimens in lateral view. Partial sequences of the gene cytochrome c oxidase I were obtained for 129 specimens representing 11 species. Based on the consistent results retrieved from the morphologic and molecular analyses, we recognized six species of Centropomus from the Atlantic coast (C. ensiferus, C. irae, C. parallelus, C. pectinatus, C. poeyi and C. undecimalis). Centropomus mexicanus is treated as a junior synonym of C. parallelus. Six species from the Pacific coast are also tentatively recognized (C. armatus, C. medius, C. nigrescens, C. robalito, C. unionensis, and C. viridis), however further studies on the Pacific species are still needed. Information on type material, diagnosis, distribution, and taxonomic comments are provided for each species. An identification key to the species of Centropomus is presented.