CO1 Sequences Research Articles

An integrative taxonomic study of north temperate Cotesia Cameron (Hymenoptera, Braconidae, Microgastrinae) that form silken cocoon balls, with the description of a new species

Using CO1 sequence analysis, we investigated the relationships of Western Palearctic and Nearctic Cotesia that spin aggregated cocoons in the shape of a ball, and as adults are morphologically very similar. The analysis included the conceptual taxa C. tibialis, C. ofella, C. vanessae, C. ruficrus, C. xylina and C. yakutatensis, as well as the newly described species C. trivaliaesp. nov. The examined specimens of C. tibialis, C. ofella, C. vanessae, C. ruficrus and C. trivaliaesp. nov. were collected in several European countries, and C. xylina and C. yakutatensis in Canada and the USA. Molecular analyses showed that C. ruficrus is not closely related to the other studied taxa. Based on the genetic distances as well as biology and morphology, C. vanessae and C. ofella are confirmed as solid taxa. The species C. yakutatensis comprises two entities. Having 8 haplotypes, C. tibialis also emerges as a species complex, divided into two clusters. With 26 detected haplotypes, C. xylina shows the highest diversity, being composed of three segregates. The conceptual species C. tibialis, C. xylina and C. yakutatensis seem to be species complexes containing several candidates for recognition as distinct species. One from the European C. tibialis complex is here described as new, and the impediments to be overcome before the description of further species are outlined.

Genetic Diversity of White-spotted Rabbitfish (Siganus canaliculatus) on Different Seagrass Habitats in Inner Ambon Bay, Indonesia Based on Mitochondrial CO1 Sequences.

This study aims to analyse the genetic diversity of Siganus canaliculatus in the Inner Ambon Bay (IAB) waters. DNA of S. canaliculatus specimens collected from IAB was extracted from tissues using a Tissue Genomic DNA Mini Kit, and partial CO1 genes were amplified using pair of universal primers. Genetic distances were determined by Kimura 2-parameter, and phylogenetic trees were constructed using the neighbour-joining method in MEGA 10.2.2 software. Arlequin software was used to analyse Fixation Index (Fst) and Analysis of Molecular Variance (AMOVA). There are three SNPs of S. canaliculatus from IAB that distinguish GenBank sequence data from S. canaliculatus. In Tanjung Tiram population group, contained three specific 677 (A), 679 (G), 703 (T) sites and two 693 (G), 714 (A) sites for the Nania population. Haplotype and nucleotide diversity of each population range from 0.000 to 1,000 and 0.000 to 0.004. Intra- and inter-population genetic differentiation were 21.19% dan 78.81%, respectively. Intra- and inter-population genetic distances were in range of 0.40-1.13 and 0.00-0.37, respectively. The pattern and direction of tidal currents as a link or barrier to spatial distribution and connectivity of S. canaliculatus larvae between seagrass habitats, as well as the presence of different anthropogenic pressures in each seagrass habitat, are thought to influence the genetic characteristics (genetic diversity, genetic variation, genetic differentiation and genetic distance) of S. canaliculatus populations in IAB waters. The results of this study provide information about the urgency of habitat-based fisheries management to support sustainable utiliation.s.

Hydroporus queneyi sp. n. from southern France, a new semi-subterranean diving beetle of the Hydroporus normandi-complex (Coleoptera, Dytiscidae, Hydroporini).

Hydroporus queneyi sp. n. is described from the area of Montpellier in southern France. It is a member of the Hydroporus normandi-complex (within the H. memnonius-group) and shares with other species of the complex the typical suite of morphological features associated with a semi-subterranean ecology. The new species differs from all previously known species of the complex by the antennomeres VXI distinctly darkened, and by a diagnostic combination of features notably of the habitus, surface sculpture and pubescence, aspect of the metacoxal lines and posterior wing venation. Its morphology is compared with that of related species, as well as described and illustrated. Collecting circumstances for the new species are described and an updated map of the distribution of H. normandi-complex species is provided. Newly produced partial sequences of the mitochondrial marker CO1 from specimens of H. queneyi sp. n., H. galloprovincialis Manuel, 2013 and two subspecies of H. normandi Rgimbart, 1903 were analysed together with publicly available sequences. In the resulting CO1 tree, haplotypes from the respective morphospecies are well separated within the H. normandi-complex, and H. queneyi sp. n. is positioned closer to the Balearic Islands endemic H. lluci Fery, 1999 than to its continental relatives H. galloprovincialis and H. normandi.

Patterns in antipredator armature reduction and maintenance in isolated spring populations of an amphipod crustacean.

Organisms colonizing new habitats can undergo adaptive change due to novel selective landscapes encountered in the new environment. Examples in nature where the development of the same traits has repeatedly occurred on multiple independent occasions upon colonizing a novel habitat represent instances of parallel evolution. Here we test whether the colonization of spring habitat by the principally lacustrine amphipod crustacean Pallaseopsis quadrispinosa has resulted in parallel evolution in armature traits using empirical data on morphology and mitochondrial DNA and through a breeding experiment. Analysis of mtDNA CO1 sequences shows that the spring populations share no common history and have evolved in isolation from each other and from their neighbouring lake populations since deglaciation approximately 12,000 years ago and are now fixed for different haplogroups. Dorsal spines and lateral projections were absent or less developed in all spring populations than in lake populations. Variation in armature development also could be explained by predator presence as populations with fish predators exhibited more developed spines than those without fish. In a laboratory breeding experiment, hybrid Spring × Lake F1 offspring had intermediate development of armature compared to offspring of Lake × Lake and Spring × Spring matings. The results support the hypothesis that armature reduction has independently evolved on multiple occasions in P. quadrispinosa. Recent research has questioned the degree to which parallel evolution actually explains variance in traits. Taking into account the predation regime, sexual dimorphism and mineral composition of the trait, a more precise understanding of the factors influencing parallel evolution emerges.

Short-legged daddy-long-leg spiders in North America: the genera Pholcophora and Tolteca (Araneae, Pholcidae)

The North American-Caribbean genera Pholcophora Banks, 1896 and Tolteca Huber, 2000 are representatives of Ninetinae, a group of small, cryptic, and thus poorly known pholcid spiders. We present the first comprehensive revisions of the two genera, including extensive SEM data and descriptions of seven new species from Mexico (Pholcophora mazatlan Huber sp. nov., P. papanoa Huber sp. nov., P. tehuacan Huber sp. nov., Tolteca huahua Huber sp. nov., T. manzanillo Huber sp. nov., T. oaxaca Huber sp. nov., and T. sinnombre Huber sp. nov.). We add new CO1 sequences of nine species to previously published molecular data and use these for a preliminary analysis of relationships. We recover a North American-Caribbean clade including ‘true’ (mainland) Pholcophora, Tolteca (Mexico), and a Caribbean clade consisting of the genus Papiamenta Huber, 2000 (Curaçao) and Caribbean ‘Pholcophora’. First karyotype data for Tolteca (2n♂ = 13, X1X2Y and 15, X1X2Y, respectively) reveal a strong reduction of the number of chromosome pairs within the North American-Caribbean clade, and considerable karyotype differentiation among congeners. This agrees with considerable CO1 divergence among species of Tolteca but contrasts with very inconspicuous morphological divergence. Environmental niche analyses show that the widespread P. americana Banks, 1896 (western USA, SW Canada) occupies a very different niche than its Mexican congeners and other close relatives. Caribbean taxa also have a low niche overlap with ‘true’ Pholcophora and Tolteca, supporting the idea that Caribbean ‘Pholcophora’ are taxonomically misplaced.

In silico exploration of the potential barcode DNA in Anopheles sp., a malarian vector from Indonesia

<span>Malaria is an infectious disease caused by <em>Plasmodium</em> and transmitted to humans through the <em>Anopheles</em> mosquito vector. The large diversity of <em>Anopheles</em> in Indonesia, which consists of similar complex species, makes it difficult to identify species based on morphological characteristics. Therefore, it is necessary to have another approach to identifying species based on molecular characteristics using DNA molecular markers. This approach becomes important as a basis for vector-based malaria control efforts. This research aims to explore potential DNA barcodes based on in silico studies as a reference for DNA barcoding analysis of <em>Anopheles</em> species in Indonesia. The data sequences of CO1 and ITS2 from <em>Anopheles</em> sp. were collected on the NCBI database. The sequence alignment was performed using CLUSTALX2. The construction of a phylogenetic tree was carried out using MEGA XI. Data analysis was performed by observing the construction of phylogenetic trees, bootstrap scores, and genetic distance. The data sequence in NCBI shows that 10 species of the genus <em>Anopheles</em> as malaria vectors have been studied in Indonesia. Sequence alignment of the 10 species based on CO1 and ITS2 markers showed that ITS2 markers had higher genetic variation than CO1. Therefore, the ITS2 sequence has the potential to be a DNA barcode for the molecular identification of <em>Anopheles</em>.</span>

Integrative taxonomy provides evidence for a cryptic lineage in the velvet worm Peripatopsis birgeri species complex (Onychophora: Peripatopsidae) in KwaZulu-Natal, South Africa

During the present study, species boundaries in the velvet worm Peripatopsis birgeri species complex in KwaZulu-Natal, South Africa, were examined with the use of DNA sequence data, gross morphology, scanning electron microscopy (SEM) and ecological niche modelling. Mitochondrial CO1 and nuclear 18S rRNA sequence data were used to generate a phylogeny using both a Bayesian inference and maximum likelihood approaches. Both the CO1 sequence data and the combined DNA sequence topology (CO1 + 18S rRNA) revealed the presence of two geographically distinct clades within the P. birgeri species complex. Results from three species delimitation methods (GMYC, PTP and ASAP), were incongruent in determining the number of species within the species complex and generally overestimated the number of operational taxonomic units. The latter result can be attributed to the marked genetic structure within the species complex, a result corroborated by the CO1 haplotype network and statistically significant F ST values. Divergence time estimation suggests that the two clades diverged during the Plio/Pleistocene. Niche modelling revealed that the two clades were differentially impacted by bioclimatic variables and occupied different habitats. Gross morphological characteristics, such as leg pair numbers and colour revealed no fixed differences between the two clades, however, a creamy white headband/collar occurred exclusively in specimens of clade 1 (P. birgeri). In contrast, SEM revealed fixed dorsal and ventral scale rank differences between the two clades. The results corroborate the presence of a novel species within the P. birgeri s.s. species complex. Peripatopsis birgeri s.s. is revised and restricted to the southern Drakensberg and a new species, P. polychroma sp. nov. (clade 2), from the northern Drakensberg and adjacent Afrotemperate forests in the interior of KwaZulu-Natal is described. https://zoobank.org/urn:lsid:zoobank:org:pub:569557AB-8BC8-49B6-B8AA-96507371297B

DNA barcoding and misidentification of some marine fish species in Nigerian industrial trawl fishery

Identification of marine fishes across their geographical distribution is based primarily on morphological features. The ability of marine fishes to adapt to environmental changes sometimes leads to morphological differences that might give rise to wrong or misidentification of the fishes, unlike genetically based identification. Fish samples were collected with a trawl net used by demersal trawlers in Nigerian coastal waters between N 4.19823⁰ E 8.29929⁰ and N 6.18855⁰ E 3.14797⁰. The average length of the COI nucleotide sequences was approximately 584 bp. A total of 30 CO1 sequences were obtained from 18 fish species within 12 families with 97–100% identity with comparison to the Genbank database and BOLD. The average divergence within a species is 4.47%, 6.10% within a genus, and 15.94% within a family, while the maximum within a species and genus is 17.54% and 19.20% within a family. Four (4) species in the Nigerian marine environment have not been sequenced before in this study: Caranx fischeri, Pseudotolithus senegallus, Lagocephalus guentheri, and Sphyraena ensis. These findings will contribute to the barcode database of global marine fish species identification, provide baseline data for marine fishes in Nigerian waters based on the CO1 region, and serve educational purposes in universities, research institutes, fishery managers, and fish stock assessment.

DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity.

The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and 'species groups' within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include 'species-complexes' previously considered as a single taxon. Our results revealed the presence of three species groups, 'C. amplexus', 'C. conspicillatus' and 'C. haematopterus' and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.

Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea).

The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.

Revisit of the taxonomic status of Bos genus with special refference to north eastern hilly region of India

North-eastern India has diverse Bos genus endemic animals which include Siri (Bos indicus), Yak (Bos grunniens) and Mithun (Bos frontalis). But very little is known about their origin and taxonomic position. Hence, a taxonomic revisit of the genesis needed to confirm their position in the family Bovidae. So, the present study focuses on molecular cataloguing through DNA barcoding and phylogenetic relationships. The generated CO1 sequences of Bos indicus, Bos grunniens, and Bos frontalis were analyzed through similarity search, Species delineation approach like K2P Distance, Neighbour-Joining tree and ML approaches to identify their taxonomic position with respect to global published data. The NJ tree revealed cohesive clustering of Bos indicus with the pre-existing sequences of zebu and taurine but distinct from other congeners. The collected specimen of Bos frontalis clustered distinctly from other congeners and failed to cluster with Bos gaurus, which nullifies the previous report of Bos frontalis as a domesticated form of Bos gaurus. Similarly, Bison bison clustered very closely with Bos grunniens as their nearest neighbour. This observation was confirmed by ML phylogeny. Our findings confirmed the Siri's species status as Bos indicus. Similarly, Bos frontalis is a different species within the genus Bos but not the domesticated form of Bos gaurus. The close clustering of Bos grunniens and Bison bison supported the previous reports, which suggest that the genus Bison should be regarded as a synonym of the genus Bos. Thus, the present study strongly recommends the revisiting of bovine taxonomy.

Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences

An additional description of the Misol snake eel Yirrkala misolensis (Günther, 1872) is reported on the basis of 9 specimens collected from Dong-gang and Ke-tzu-liao, southwestern Taiwan. The species was previously reported from Indonesia and Australia and then extends northward to Taiwan and Japan, and was lacking adequate characterization on morphology. A detail description, fine condition of fresh photographs and 4 partial CO1 sequences are provided for the first time.

Molecular detection of Candidatus Rickettsia colombianensi in ticks (Acari, Ixodidae) collected from herpetofauna in San Juan de Carare, Colombia.

Knowledge about ticks and Rickettsiae in Colombia is still limited and the areas of the country where studies have been conducted are scarce. In this study, ticks (Acari, Ixodidae) associated with reptiles and amphibians in San Juan de Carare, Santander department, were morphologically and molecularly identified and tested for the presence of Rickettsia. For the molecular characterization of ticks, CO1, 12S and 16S sequences were generated and compared with other sequences available in genbank. Our analyses confirmed that the collected ticks were Amblyomma dissimile, and we provide the first report of this species parasitizing the snake Leptodeira septentrionalis. Of the samples analyzed, 69% were positive for Rickettsia sp. using the gltA, ompA and sca1 genes. Rickettsia sequences generated in this study were also compared to sequences downloaded from genbank by Bayesian inference (BI) and maximum likelihood (ML) phylogenetic analyzes. The presence of a single Rickettsia species, Candidatus Rickettsia colombianensi, was identified. This study expands the knowledge regarding the distribution of A. dissimile ticks and Rickettsiae in Colombia.

Atypus karschi Dönitz, 1887 (Araneae: Atypidae): An Asian purse-web spider established in Pennsylvania, USA

The mygalomorph spiders of the family Atypidae are among the most archaic spiders. The genus Atypus Latreille, 1804 occurs in Eurasia and northern Africa, with a single enigmatic species, Atypus snetsingeri Sarno, 1973, known only from a small area in southeastern Pennsylvania in eastern USA. A close relationship to European species could be assumed based on geographic proximity, but A. snetsingeri more closely resembled Asian species. This study was undertaken to learn more about the genetics of A. snetsingeri, its habitat requirements and natural history. Molecular markers (CO1 sequences) were compared to available data for other atypids and showed that A. snetsingeri is identical with A. karschi Dönitz, 1887 native to East Asia. Natural history parameters in Pennsylvania were also similar in every respect to A. karschi in Japan, therefore, we propose that the spider is an introduced species and the specific epithet snetsingeri is relegated to a junior synonym of A. karschi. Cytogenetic analysis showed an X0 sex chromosome system (42 chromosomes in females, 41 in males) and we also detected nucleolus organizing regions and heterochromatin, the latter for the first time in the Atypoidea. In Pennsylvania the spider is found in a variety of habitats, from forests to suburban shrubbery, where the above-ground webs are usually attached vertically to trees, shrubs, or walls, although other webs are oriented horizontally near the ground. Prey include millipedes, snails, woodlice, carabid beetles and earthworms. Atypus karschi is the first known case of an introduced purse-web spider. It is rarely noticed but well-established within its range in southeastern Pennsylvania.

DNA barcode analysis of the endangered green turtle (Chelonia mydas) in the breeding grounds of Badagry, Lagos, Nigeria

The Nigerian coastline is long and heavily populated. It is also the nesting site of a huge numbers of species that are dependent on that ecosystem for their reproduction cycle. Artisanal fishermen and the local populace are dependent on these species as a cheap and alternative source of protein. The Sea Turtles having been classified as threatened by the IUCN are a major part of that ecosystem. Currently, there is however a dearth of research works on the species. The usefulness of the DNA barcoding region (CO1) of the mitochondrial genome is used to analyze populations of Chelonia mydas along Badagry beach in Lagos, Nigeria. Seven samples were obtained and CO1 sequences were generated from them. Twenty seven more sequences were harvested from the GenBank of which only five were used in the final analysis either because there were errors (insertions, deletions or stop codons) or because of redundancies. A Six hundred and Eighteen (618bp) index free sequences was obtained. The intraspecific divergence in the Nigerian samples was very low, being between 0.00 and 0.002, while the intraspecific distance when the other sequences were added increased a bit ranging from 0.002 to 0.54. Neighbor- joining phylogenetic tree produced two distinct clade, with the Nigerian samples being clearly mapped into one with bootstrap value of 100% while others mapped into another. The best substitution model is TN93+G. The Tajima index was also very low indicating a population with very low genetic divergence. The average codon usage also followed the pattern A (29.3) > C (28.7) > T (27.3)> and a G (14.8). An expansion of the sampling points and increase number of samples is recommended for a more robust ideal of the relatedness within and without.

What complete mitochondrial genomes tell us about the evolutionary history of the black soldier fly, Hermetia illucens

BackgroundThe Black Soldier Fly (BSF) Hermetia illucens is a cosmopolitan fly massively used by industrial companies to reduce biowaste and produce protein and fat for poultry and aquaculture feed. However, the natural history and the genetic diversity of the BSF are poorly known. Here, we present a comprehensive phylogeny and time tree based on a large dataset of complete mitochondrial genomes better to understand the evolution and timing of the BSF.ResultsIn this study, we analyzed 677 CO1 sequences derived from samples found all over the five continents, leading us to discover 52 haplotypes, including ten major haplotypes. This worldwide cryptic genetic and genomic diversity is mirrored at a local scale in France, in which we found five major haplotypes sometimes in sympatry. Phylogenetic analyses of 60 complete mitochondrial genomes robustly resolved the phylogeny of the major BSF haplotypes. We estimate the separation events of the different haplotypes at more than 2 million years for the oldest branches characterizing the ancestral split between present North American lineages and the other highly diverse south-central American clades, possibly the following radiation beyond the isthmus of Panama northwards. Our data confirm that this North American lineage ultimately gave birth to almost all commercial BSF stocks that participated in the worldwide BSF dissemination through farm escapements.ConclusionsOur data resolve the phylogenetic relationships between the major lineages and give insights into the BSF’s short and long-term evolution. Our results indicate that commercial BSF stock’s genetic and genomic diversity is very low. These results call for a better understanding of the genomic diversity of the BSF to unravel possible specific adaptations of the different lineages for industrial needs and to initiate the selection process.

Integrative Taxonomy and Synonymization of Aculus mosoniensis (Acari: Eriophyidae), a Potential Biological Control Agent for Tree of Heaven (Ailanthus altissima).

Simple SummaryTree of heaven, Ailanthus altissima, is a deciduous tree indigenous to China and introduced for ornamental purposes into North America and Europe. It shows a highly invasive profile in field, urban, and suburban areas, posing a serious threat to ecosystems in the introduced ranges. The current management of this noxious infesting plant by mechanical and chemical measures remains ephemeral and incomplete. A multi-tactic approach emphasizing classical biological control appears highly relevant. Eriophyid mites are well known for their high specificity and for the impact caused to the associated hosts, resulting in relevant potential biological control agents of infesting plants. The partially unresolved taxonomy of the eriophyid mite species reported on the tree of heaven is currently seen as an impediment to their further concern as biocontrol agents. This paper investigated morphological and molecular characters of Aculus mosoniensis in order to better clarify its taxonomic status. A paratype specimen of Aculops taihangensis was also studied, and this mite species was reassigned to the genus Aculus. The strong congruence between morphological and molecular analyses for all mites collected on tree of heaven in Europe led to the conclusion that A. mosoniensis is a junior synonym of Ac. taihangensis.The taxonomy of Aculus mosoniensis appears to be an unresolved question and its clarification is required, owing to the potential relevance of this mite species as a biological control agent of the tree of heaven. This paper is aimed at giving accurate details on a previously and shortly announced synonymization with Aculops taihangensis, using a morphological and molecular approach. A fusiform morph of A. mosoniensis was distinguished from a vermiform morph and this latter was recognized as deutogyne, which was herein documented. Phylogenetic relationships between Chinese Ac. taihangensis and all A. mosoniensis mites collected in twenty localities in Europe were examined through the analysis of the mitochondrial cytochrome c subunit I (CO1) protein and the nuclear ribosomal internal transcribed spacer 1 region (ITS1). CO1 sequences of Ac. taihangensis from the Shandong province in China and those from mites collected in Austria and Slovenia were 100% identical; the ITS1 sequence of an Ac. taihangensis paratype matched for 99.8% with those obtained from protogynes and deutogynes of A. mosoniensis collected in Italy. All these data supported the announced synonymization of A. mosoniensis with Ac. taihangensis. Aculus mosoniensis was found genetically variable, with five CO1 haplotypes in Europe (becoming eight along with those of Ac. taihangensis) clustering in two highly supported maternal lineages and eight ITS1 haplotypes (becoming nine along with those of Ac. taihangensis) distributed in four supported clades. No overlap between intra- and interspecies distances was observed for both markers and all studied A. mosoniensis populations clustered in one monophyletic mitochondrial clade, suggesting that only one single species might occur in Europe. However, more mite clades may be related to more tree of heaven biotypes with potential ecological differences, which might have potential effects on the biological control and should be investigated.

A remarkable new species of the genus Hydaticus from Madagascar, with an identification key for Malagasy species of the genus (Coleoptera: Dytiscidae: Dytiscinae)

Summary Hydaticus (Prodaticus) mangamanga n. sp. is described from a single sampling site in the south-eastern part of Madagascar Central Highlands, near Ranomafana. The new species is unique among the known species of the genus Hydaticus in that the last visible abdominal ventrite is strongly modified and differentiated between sexes, and is also quite unusual in paramere configuration. Analysis of partial CO1 sequences revealed that H. mangamanga belongs to the leander-group and is genetically close to the Malagasy region endemic H. inconspicuus Régimbart, 1895 stat. rev. with only around 1.5% of sequence divergence, providing the first instance of a sister-group relationship between two Hydaticus species endemic from the Malagasy region. However, morphologically these two species differ considerably. They are illustrated (habitus, structures, male genitalia) and compared in detail. Collecting circumstances for H. mangamanga are described and a map of its known distribution is provided. A lectotype is designated for H. inconspicuus; this name is re-established as valid for this species, and the name H. kolbei Branden, 1885 used in the recent literature is considered of doubtful identity. An identification key is provided for all Hydaticus (Prodaticus) species known from Madagascar, with accompanying illustrations of median lobes of aedeagus in lateral view.

Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences

Abstract. Mahrus H, Idrus AA, Zulkifli L. 2022. Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences. Biodiversitas 23: 2433-2443. This study aimed to identify anchovy samples genetically and evaluate their phylogenetic relationship to anchovies using the CO1 genetics markers. Fragment amplification of COI gene anchovy used a pair of COI commercially available primer with a length amplicon of about 693 base pairs (bp), coding for 231 amino acids successfully. The reconstruction of the phylogenetic tree with the neighbor-joining (NJ) method using Kimura 2 Parameters (K2P) by employing a bootstrap of 1000 replications. The genetic distance analysis between 19 fishes species in different families and 13 species in the genera Spartelloides acceded from NCBI indicated the closest distance between anchovy samples from the southern waters of Lombok and Spratelloides delicatulus from Australia is 0.02. The comparisons results of homology with the NCBI and the BOLD database show the anchovy sample has similarities to the CO1 sequences of S. delicatulus with a similar of 99%. The results of the phylogenetic tree analysis showed that the anchovy samples from the southern waters of Lombok were in the same clade as S. delicatulus from Australia. The study concluded a fish sample of anchovy from the southerly waters of Lombok was a closed related species to S. delicatulus.

MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

AbstractAnalysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness of this approach depends on the accuracy of taxonomic reference databases. The MIDORI databases, first released in 2017, were built to improve accuracy for mitochondrial metazoan (animal) sequences. MIDORI has now been significantly improved and renamed MIDORI2 (available at http://www.reference‐midori.info). Like MIDORI, MIDORI2 is built from GenBank and contains curated sequences of thirteen protein‐coding and two ribosomal RNA mitochondrial genes. Coverage has been substantially expanded to cover all eukaryotes, including fungi, green algae and land plants, other multicellular algal groups, and diverse protist lineages. MIDORI2 also now includes not only species with full binomials, but also taxa referred to by genus with species left unspecified (“sp.”). Another new feature is the updating of the databases approximately every two months with version numbers corresponding to each new GenBank release. Additional potentially erroneously annotated sequences have also been removed. Finally, the ability to export data files to BLAST+ has been added to the original ability to export preformatted data to five taxonomic assignment programs, and databases of amino acid sequences are also made available for protein‐coding genes. As a technical validation, we conducted a preliminary comparison of the performance of MIDORI2 with five taxonomic assignment programs. Results suggest that BLAST+ top hits performed better for assigning CO1 sequences than alignment‐free methods based on compositional features. Comparing MIDORI2 with two other commonly used curated databases of mitochondrial sequences, CO‐ARBitrator and BOLD, we show that MIDORI2 includes sequences from a broader range of metazoan and non‐metazoan taxa. Overall, in many contexts, MIDORI2 offers clear advantages: a higher diversity of taxa than other databases, a variety of user‐friendly features, and regular updates. MIDORI2 is particularly well‐suited for environmental DNA studies that target mitochondrial genes with broad primers.