COI Barcode Region Research Articles

Zealastoa Quicke & Ward, gen. nov., a new basal cyclostome braconid wasp (Hymenoptera: Braconidae) from New Zealand

AbstractThe Mesostoinae are an almost entirely Gondwanan subfamily of Braconidae, known from Australia, New Zealand and South America (extending into MesoAmerica). They are morphologically and biologically diverse and, together with Aphidiinae and Maxfischeriinae, are the sister group to all other extant cyclostome braconids. Here we describe and illustrate a new genus, Zealastoa Quicke & Ward, gen. nov., and three new species: Z. waitakerensis Quicke & Ward, sp. nov., Z. hirta Belokobylskij, Quicke & Ward, sp. nov., and Z. multiarticulata Belokobylskij, Quicke & Ward, sp. nov., all from New Zealand. Molecular phylogenetic analysis based on combined nuclear 28S rDNA D2‐D3 expansion region and the barcoding region of mitochondrial COI strongly support a monophyletic clade comprising the endemic New Zealand genera (Doryctomorpha Ashmead, Metaspathius Brues, Rhyssaloides and Zealastoa gen. nov.) as being the sister group to all other members of the subfamily.

First record of Tettigometridae (Hemiptera: Fulgoromorpha) from Pakistan: description of a new species including barcode identification.

Tettigometra ziaratensis sp. nov. is described from Ziarat, Baluchistan, Pakistan; it is the first record of the genus Tettigometra Latreille, 1804 and the family Tettigometridae from this country. Sequence data for the barcoding region of the mitochondrial gene COI for this new species was obtained and deposited in GenBank.

Oxynoemacheilus cilicicus, a new nemacheilid loach from the Göksu River in southern Anatolia (Teleostei: Nemacheilidae)

Oxynoemacheilus cilicicus, new species, is described from the Göksu, Seyhan and Ceyhan rivers in southern Turkey. It is distinguished from other Oxynoemacheilus species in the Eastern Mediterranean Sea basin by possession of an incomplete lateral line, terminating before the vertical of the dorsal-fin origin or slightly behind the dorsal-fin base, a deeply emarginate caudal fin, no suborbital groove in male individuals, and a series of dark-brown bars on the flank not interrupted along the lateral line. Molecular data suggest that Oxynoemacheilus cilicicus is characterised by 22 variable nucleotide substitutions and a minimum K2P distance of 4.09% with O. panthera in the mtDNA COI barcode region.

Real-time PCR for identification of five species of Cryptolestes based on COI barcode region

Cryptolestes(Coleoptera: Laemophloeidae) are economically important pests, which damage stored products in granaries and mills. Because it is difficult to distinguish Cryptolestes species morphologically, we develop here a high sensitivity real-time PCR method for distinguishing five species of Cryptolestes (C. ferrugineus, C. pusillus, C. turcicus, C. pusilloides and C. capensis). The lower limit of DNA concentration required for species identification is 0.1 ng/μl for C. ferruginues and C. pusilloides, and 0.01 ng/μl for C. pusillus, C. turcicus, and C. capensis. This method successfully determined species assignments for previously unidentified Cryptolestes spp. Collected from the field and will facilitate Cryptolestes identification in the field of plant quarantine and stored product protection.

Seminemacheilus dursunavsari, a new nemachelid species (Teleostei: Nemacheilidae) from Turkey

Seminemacheilus dursunavsari , new species, is described from the Goksu River drainage, Eastern Mediterranean Basin, Konya Province, Turkey. This species is distinguished from the other members of the genus by a combination of the following characters: having irregular molted dark black spots and blotches on flanks, lacking blotches and spots on dorsal faces of head and ventral part of body, possessing fused black spots at base of caudal fin, a saddle-like black spot on the dorsal-fin origin, and blunt snout. Seminemacheilus dursunavsari n. sp. is also diagnosed from S. lendlii , S. ispartensis and S. ahmeti by 13 fixed, diagnostic nucleotide substitutions in the mtDNA COI barcode region, and a K2P genetic distance of 5.8, 5.6 and 4.7%, respectively.

Two new dipluran species unearthed from subterranean habitats of the Canary Islands (Arthropoda, Hexapoda, Entognatha)

Two new dipluran species of the family Campodeidae have been unearthed in the Canary Islands. Remycampa herbanicasp. nov. was found in a highly threatened lava tube on Fuerteventura island. It is related to the soil-dwelling northwest African Remycampa launeyi that also inhabits four of the Canary Islands. The two known Remycampa species are characterized by a torsion of the labial palps. They differ chiefly in the distribution of macrosetae and in the features of cave adaptation of R. herbanica, i.e. elongation of body and appendages, and a higher number of olfactory chemoreceptors with a coniform shape unique within campodeids. Spaniocampa relictasp. nov. was collected in the mesovoid shallow substratum (MSS) and has been assigned to a formerly monotypic genus that includes the soil-dwelling Spaniocampa prima from the Republic of Guinea. The two species differ in the number of abdominal macrosetae. Females of S. relictasp. nov. have small setae arranged in groups along the posterior border of the first urosternite. These structures of unknown function have never been described in other campodeid species. Sequencing the COI barcode region of R. herbanica has been produced but it proved insufficient to identify closest relatives. The two new hexapods from subterranean habitats raise the Canarian campodeid fauna to six species. Five of them are living in soil and/or MSS, whereas the cave-adapted R. herbanica is known only from a single, particularly endangered lava tube distant from other caves.

New species of Silhouettea (Teleostei: Gobiidae) from Qeshm Island, Iran andthe DNA barcoding of the Persian Gulf and Oman Sea gobies.

Silhouettea ghazalae sp. nov. is described from Qeshm Island, Persian Gulf. Silhouettea ghazalae sp. nov. is distinguished from congeners by having: small mental fold present on chin, head length 31.4-32.4% of standard length, head width 24.5% of standard length, second dorsal fin I/11, anal fin I/13, breast with large cycloid scales, predorsal area naked, suborbital row b anteriorly beginning below anterior edge of pupil, posteriorly ending below pore β, suborbital row c anteriorly extending more than row b and posteriorly extending less than row b, suborbital row cp oblique with four papillae, body with four ill-defined midlateral blotches and the fifth a triangular mark on the caudal fin base, no clearly defined pale saddles on back, and the first dorsal fin pigmented with dots and with dark blotch present anteriorly. A key to Silhouettea species is provided. A dataset including novel and publicly available mtDNA COI sequences of 12 species from the Persian Gulf and Oman Sea gobies belonging to eight genera have been assembled in order to provide a reference dataset for DNA barcoding studies. The new species is further characterised by a minimum K2P distance of 21% to its closest relatives in our dataset, Cabillus tongarevaein the mtDNA COI barcode region.

Description of a new snake eel Ophichthus olivaceus (Teleostei: Anguilliformes, Ophichthidae) from the Red Sea.

A new species of snake eel Ophichthus olivaceus is described based on two specimens trawled from a depth of 35-63 m from a soft substratum off Jizan, Red Sea coast of southern Saudi Arabia. It differs from its congeners by the following combination of characters: vertebrae 141-145; tail moderately short (2.15 in TL); head short (9.6-11.1 in TL); uniserial teeth in jaws and on vomer; pectoral fins slightly elongate, not lanceolate, upper rays longer than the lower; dorsal-fin origin above middle of pectoral fin; and a generally uniform, dark tan body with an olivaceous hue shading to tan or pale orange ventrally, with two pale yellow blotches above pectoral-fin base, snout and lower jaw dark brown, and olivaceous median fins. Its divergence from other mitochondrial-analyzed species is shown by phylogenetic analysis of the mitochondrial COI barcoding region. A key to the Indian Ocean species is provided.

A subterranean ant Acanthostichus Mayr, 1887 is revealed in Costa Rica

In this study, pinned insect specimens derived from Malaise traps in Costa Rica were identified using a collaborative process, resulting in a significant addition to our understanding of the range of a rare Neotropical ant genus. The specimens were imaged and the COI barcode region of mitochondrial DNA was sequenced. The images and sequence data were shared in an open access database. Public exposure from such a digitally based approach to biodiversity analysis allowed us to collaboratively uncover the first known Costa Rican occurrence of the subterranean ant genus Acanthostichus, filling in a heretofore confusing hole in its geographic range.

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding.

Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic “protists,” with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro‐eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro‐eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.

Characterization of Martensia (Delesseriaceae; Rhodophyta) from shallow and mesophotic habitats in the Hawaiian Islands: description of four new species

ABSTRACTFifty-six specimens of the red algal genus Martensia from the Main and Northwestern Hawaiian Islands, representing both shallow (36 specimens from 0–20 m depth) and mesophotic habitats (20 specimens from 62–93 m depth), were collected and characterized using morphological and molecular analyses. Phylogenetic analyses of the rbcL gene resolved five distinct clades of Martensia from the Hawaiian Islands, of which none could be attributed to the two previously used taxonomic names for this flora (M. fragilis Harvey and M. flabelliformis Harvey ex J.Agardh). Analyses of the COI barcoding region were consistent with rbcL trends, although fewer specimens amplified and sequenced for this marker. Four rbcL clades (lineages 1–4) were distinct from each other and from other described species of Martensia based on both phylogenetic position and morphological characters, and are here described as new species: Martensia abbottiae A.R.Sherwood & S.-M. Lin sp. nov., Martensia hawaiiensis A.R.Sherwood & S.-M. Lin sp. nov., Martensia tsudae A.R.Sherwood & S.-M. Lin sp. nov., and Martensia lauhiekoeloa A.R.Sherwood & S.-M. Lin sp. nov. Lineage 5 is attributable to M. albida Y.Lee. All five species in the Hawaiian flora occur in mesophotic habitats, while M. hawaiiensis, M. tsudae, and M. albida also inhabit shallow waters of the Main Hawaiian Islands. This study provides additional support for the degree of uncharacterized biodiversity from mesophotic depths in the Hawaiian Archipelago.

Garra roseae, a new species from the Makran region in southern Iran(Teleostei: Cyprinidae).

Garra roseae, new species, is described from the stream Tang-e-Sarhe in the Iranian Makran region. It is distinguished from its congeners in the Middle East by lacking barbels, having a small mental disc, 42-58 total scales along the lateral line, 24-30 scales along the predorsal midline, and 20-24 circumpeduncular scales. It is further characterised by having five diagnostic nucleotide substitutions and a minimum K2P distance of 5.39% to G. rossica and 5.49% to G. nudiventris in the mtDNA COI barcode region. Garra phryne from eastern Iran is considered to be a synonym of G. nudiventris.

Paraschistura kermanensis, a new stone loach species from southeastern Iran(Teleostei: Nemacheilidae).

Paraschistura kermanensis from the endorheic Kerman-Naein basin in Iran is distinguished from its closest congeners (P. abdolii, P. delvarii, P. kessleri and P. naumanni) by lacking scales on the flanks anterior to the dorsal-fin origin, having scales on the caudal peduncle, and having the pelvic-fin origin situated anterior to or below the vertical through the dorsal-fin origin. It is also characterised by six fixed diagnostic nucleotide substitutions and a K2P nearest neighbour distance of 4% to P. abdolii in the mtDNA COI barcode region.

Scolopsis igcarensis Mishra, Biswas, Russell, Satpathy amp; Selvanayagam, 2013, a junior synonym of S. vosmeri (Bloch, 1792) (Perciformes: Nemipteridae).

Scolopsis igcarensis Mishra, Biswas, Russell, Satpathy Selvanayagam, 2013 was described from specimens collected from coastal waters of southern India and Sri Lanka. A comparison of recently collected specimens from Bangladesh, initially identified as S. igcarensis, with Scolopsis vosmeri (Bloch, 1792) showed morphological differences between the two species are minor, and that specimens of S. igcarensis in fact represent juvenile and subadult colour forms of S. vosmeri. Underwater and aquarium observations, as well as molecular data based on the COI barcode region, support this conclusion. Accordingly, S. igcarensis is regarded as a junior synonym of S. vosmeri, which is redescribed herein. Phylogenetic analysis of COI barcodes of Scolopsis specimens produced in this study, together with those available from GenBank, indicate S. vosmeri is part of a species complex which includes two additional cryptic sister species that require further taxonomic investigation.

A new leaf-mining moth, Caloptilia aesculi, sp. nov. (Lepidoptera: Gracillariidae: Gracillariinae) feeding on Aesculus chinensis Bunge (Hippocastanaceae) from China.

A new species of the genus Caloptilia associating with the Chinese horse chestnut, Aesculus chinensis Bunge (Hippocastanaceae) from China is described. The photographs of the adults, male and female genitalia, larva and pupa, the leaf mines and leaf shelters (rolls and stacks) are given. This is the first report of host association with Hippocastanaceae in the subfamily Gracillariinae. The sequence of mitochondrial COI barcoding region of this species is provided and its phylogenetic position is analyzed with other Caloptilia species.

Multiple new species: Cryptic diversity in the widespread mite species Cymbaeremaeus cymba (Oribatida, Cymbaeremaeidae)

The absence of obvious morphological differences between species impedes species identification in many groups of organisms. Such cryptic species appear to be particularly common in small-bodied animals, impacting species richness estimates.In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Phylogenetic analyses of three molecular markers, including the COI barcoding region, identified eight well supported, fairly divergent clades within C. cymba, which we consider to represent distinct species based on molecular species delimitation methods. Intraspecific variation of the COI gene was extremely low in all putative species, contradicting previous assumptions of high intraspecific diversity in oribatid mites. The frequent co-occurrence of two species on a single tree suggests an ecological micro-niche differentiation. Contrary to previous studies on oribatid mites, we find that COI is a good marker for species delimitation and its further use for barcoding of oribatids is highly recommended. Furthermore, we provide descriptions of six new Cymbaeremaeus species and designate a neotype of C. cymba.

Deep genetic differentiation between two morphologically similar species of wolf herrings (Teleostei, Clupeoidei, Chirocentridae)

Wolf herrings (Chirocentridae; Clupeoidei) are commonly found in local fish markets throughout the Indo-West Pacific region where they constitute an auxiliary source of food and income for local communities. The validity of the two species of wolf herrings, Chirocentrus dorab Forsskål, 1775 and C. nudus Swainon, 1839, is only supported by slight morphological differences. The identification of either species is challenging, especially for juveniles, and precludes accurate assessments of these natural resources at a species level. As a step towards gaining better knowledge of the genetic structure of these fishes, we examined genetic differentiation between these two species by reconstructing their entire mitogenomic sequences using high-throughput sequencing technology. We found that the mitogenome of each species shared the same gene content and order that were the same for those found in most other teleost fishes. Despite their high morphological similarity, these two species of Chirocentrus were genetically well differentiated (p-distance = 16.3% at their cytochrome oxidase I). A mitogenomic time-calibrated phylogenetic analysis showed that wolf herrings originated about 35 million years ago, and they represent a case of morphological stasis. Furthermore, comparison of published and newly determined mitochondrial COI barcode region sequences from 22 individuals revealed species-level cryptic genetic diversity within C. dorab. Altogether, these mitochondrial data are effective in discriminating species within this genus and informing population genetic relationships within species of wolf herrings.

Oxynoemacheilus cemali, a new species of stone loach (Teleostei: Nemacheilidae) from the Çoruh River drainage, Turkey.

Oxynoemacheilus cemali sp. nov. is described from the Çoruh River drainage in the eastern Black Sea basin. One molecular marker (coI), 25 morphometric and four meristic characters were analysed. Oxynoemacheilus cemali is distinguished from O. kosswigi, O. banarescui, O. samanticus and O. angorae in the Black Sea basin by having a suborbital groove in males, an axillary lobe at the pelvic-fin base, no dorsal adipose crest on the caudal peduncle, a slightly-forked caudal fin and 7-15 dark grey dorsal saddles. Morever, Oxynoemacheilus cemali is distinguished by commonly having 9-15 irregularly-shaped dark-grey bars on the flank posterior to the dorsal-fin origin or, rarely having a mottled pattern or 4-6 irregularly shaped dark-grey bars on the flank posterior to the dorsal-fin origin. Oxynoemacheilus cemali is also distinguished from the closely related species O. araxensis and O. cyri, distributed outside the Black Sea basin, by having 15 and 31 diagnostic nucleotide substitutions in the coI barcode region, respectively.

A New Genus and Species of Gelechiini (Lepidoptera: Gelechiidae) Feeding on Brazilian Peppertree

Recent efforts to discover insect biological control agents of the Brazilian peppertree, Schinus terebinthifolius (Anacardiaceae), include a new species belonging to a new genus, Spes schinella Metz, new genus, new species. We propose a hypothesis for placement of the new species among known Gelechiinae using the barcoding region of COI and targeted taxon sampling in a tree parsimony analysis, and discuss additional diagnostic morphological features for tribal placement. The new species is diagnosed, described, and illustrated.

Review and re-description of Sabanejewia species in Iran (Teleostei: Cobitidae)

The Iranian species of the genus Sabanejewia are reviewed based on morphological, osteological and molecular characters of the mtDNA COI barcode region. Two species, Sabanejewia aurata and Sabanejewia caspia are recognized and diagnoses are presented for both species. They are distinguishable through body pattern, length of caudal peduncle, snout and post orbital distance, shape of scale and suborbital spine, caudal complex skeleton and also the number of fixed, diagnostic nucleotide substitutions. Here we re-describe both Iranian spined loaches.