COI Barcoding Gene Research Articles

Two new species of the rare lobster genus Thaumastocheles Wood-Mason, 1874 (Reptantia: Nephropidae) discovered from recent deep-sea expeditions in the Indo-West Pacific

Specimens of species closely related to the rare deep-sea lobster Thaumastocheles japonicus Calman, 1913 were obtained from recent deep-sea expeditions in the West Pacific. Close examination of these specimens, as well as molecular analysis, showed that they represent two species new to science, with many morphological and significant genetic differences (barcoding gene COI sequence divergences 11.5-14.8%) between each other as well as T. japonicus. Re-examination of the specimens previously assigned to T. japonicus revealed that true T. japonicus has a more northern distribution, from Japan to the South China Sea and the Philippines. The two new species have more southern distributions with T. bipristis n. sp. restricted to the Philippines and Indonesia, and T. massonktenos n. sp. being widely distributed in the Indo-West Pacific, from the South China Sea to Madagascar and New Caledonia. The genetic data also suggest that T. dochmiodon Chan and de Saint Laurent, 1999 may represent a polymorphic male form of T. japonicus.

Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecularidentification.

A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences – almost 20% of the total – this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification.We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification.

Munidopsis lauensis Baba & de Saint Laurent, 1992 (Decapoda, Anomura, Munidopsidae), a newly recorded squat lobster from a cold seep in Taiwan.

The squat lobster, Munidopsis lauensis Baba & de Saint Laurent, 1992, is recorded from Taiwan for the first time. This species was previously known only from deep-sea hydrothermal vents in the South-West Pacific but it was now found at a deep-sea cold seep site off southwestern Taiwan. The identity of the Taiwanese material is confirmed by comparison of sequences from the barcoding gene COI. Munidopsis lauensis can be easily separated from other congeners in Taiwanese waters by the eyes bearing a strong mesiodorsal spine and a small mesioventral spine, smooth carapace, fingers of the cheliped distally spooned and fixed finger without a denticulate carina on the distolateral margin. The discovery of this species in Taiwan increases the Munidopsis fauna of the island to 38 species. A color photograph and line drawings illustrating distinctive characters are provided for the Taiwanese material.

Oligochaeta (Annelida) of the profundal of Lake Hazar (Turkey), with description of Potamothrix alatus hazaricus n. ssp..

Lake Hazar is an alkaline oligotrophic lake of tectonic origin, located in the Eastern Anatolia region in Turkey, 1248 a a.s.l. Its surface area is 80 km2, the average depth 93 m and maximum depth 205 m. The lake and its surroundings an under protection as a region of historical value. During the present study (2007-2012), samples were taken from 15 stations located at a depth of 2-200 m. Oligochaeta comprised 69% of the total invertebrate abundance. The profundal olgochaete fauna was found to consist of only three tubificid taxa, all of the subfamily Tubificinae. Potamothrix alatus hazaricus Timm & Arslan, n. ssp. was dominating anywhere down to maximum depths while Psammoryctides barbatus (Grube) and Ilyodrilus(?) sp. occurred seldom. All three are new records for Lake Hazar. Potamothrix alatus hazaricus shares the "winged" body shape in its genital region with the nominal, brackish-water subspecies P. a. alatus Finogenova, 1972, and the lateral position of the spermathecal pores and the shape of the ventral chaetae with the freshwater subspecies P. a. paravanicus Poddubnaja & Pataridze, 1989 known from Transcaucasian lakes. The mitochondrial COI barcoding gene suggests long separation between the two taxa, but the nuclear ITS region shows no variation. The generic position of Ilyodrilus (?) sp. remains obscure since its internal genitalia could not be studied.

Development of DNA chip for verification of 25 microalgae collected from southern coastal region in Korea

Countless species occur in the marine microalgal domain. Some are used as health functional foods or medical products but many species are harmful such as those that cause the red tide. Therefore, it is necessary to conduct prompt and accurate identification of microalgal species. As it is quite difficult to accurately distinguish all species in terms of morphology, we performed DNA barcoding analysis using molecular markers for more accurate and rapid screening. DNA barcoding analysis, i.e., DNA chip technology, is a powerful method for studies on microalgal taxonomy and biodiversity. We used the mitochondrial cytochrome c oxidase subunit I (mtCOI) as a barcoding gene to identify microalgal species. In this study, the diversity and phylogenetic differences among different microalgae were analyzed. Additionally, a microalgal species-specific probe was screened by 21–23 bp and the result was printed on silylated slide for use in a robotic microarrayer. As a result, we performed a DNA chip assay for each of 25 microalgal species and determined that the COI barcode gene was suitable as a marker gene, as it could identify various microalgae from the Korean South Sea by species.

Cryptic diversity among the achaetous Marionina (Annelida, Clitellata, Enchytraeidae)

This study investigates the diversity and taxonomy of a mainly marine group of species lacking chaetae currently assigned to the genus Marionina. This achaetous group includes four nominal species: M. achaeta (Hagen, 1954), M. achaeta sensu Lasserre, 1964, M. nevisensis Righi & Kanner, 1979 and M. arenaria Healy, 1979. As Lasserre's (1964) M. achaeta appears to be morphologically different from its (then) senior homonym M. achaeta (Hagen, 1954), the replacement name M. nothachaeta nom. nov. is proposed for it. We studied the genetic and morphological diversity of achaetous specimens of Marionina collected in Florida, the Great Barrier Reef, New Caledonia, Sweden, England and the Bahamas. The collection localities are almost all supralittoral and often brackish-water habitats. Parts of the mitochondrial genes 12S, 16S, COI and the nuclear genes 18S, 28S and ITS were analysed to assess the genetic variation and phylogeny of the achaetous Marionina species. The molecular data reveal one monophyletic group of 11 separately evolving lineages, and between these lineages, K2P distances in the barcoding gene COI vary between 5.4 and 25.0%. On a morphological basis, the lineages could be assigned to seven different groups (morphotypes), of which only two could be identified as described nominal taxa: M. nevisensis s. lat. (several lineages) and M. nothachaeta. Since the former taxon appears to be a complex of cryptic species around the world and the original type material no longer exists, a neotype from the Caribbean was designated for M. nevisensis s. str. The remaining achaetous lineages represent five morphologically distinct species that are left unnamed, awaiting finer morphological scrutiny and detailed comparisons with new collections of M. achaeta and M. arenaria. Summing up, the group of achaetous Marionina now seems to contain up to 13 different species, seven of which are yet to be formally described and named.

Hippolytidae and Barbouriidae (Decapoda: Caridea) collected during the Ryukyu “KUMEJIMA 2009” expedition

The present report deals with caridean shrimps from the families Hippolytidae (7 species) and Barbouriidae (1 species)collected during the KUMEJIMA 2009 expedition in the Ryukyu Islands. The deep-water hippolytid Gelastreutescrosnieri Bruce, 1990 is recorded from Kumejima based on a single female specimen, representing a considerable rangeextension of this species from New Caledonia to Japan. The opportunity is also taken to record and illustrate the firstknown male specimen of G. crosnieri, collected during the SANTO 2006 expedition off West Mavéa Island, Vanuatu. Thecolour pattern of G. crosnieri is shown for the first time. The Kumejima and Vanuatu specimens present noticeabledifferences in both morphology and colouration, but appear to be conspecific based on comparison of the barcoding geneCOI sequences. The recently described Lysmata lipkei Okuno & Fielder, 2010 is recorded for the second time, however,not representing a significant range extension of this species. The other species reported are Saron marmoratus (Olivier,1811), Saron neglectus De Man, 1902, Thinora maldivensis (Borradaile, 1915), Thor amboinensis (De Man, 1888), Tozeuma armatum Paul’son, 1875 (Hippolytidae), and Parhippolyte misticia (Clark, 1989) (Barbouriidae).

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

Summary1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution.2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass‐PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’.3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within‐community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding.4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.

Morphological and genetic variability in Hippolyte obliquimanus Dana, 1852 (Decapoda, Caridea, Hippolytidae) from Brazil and the Caribbean Sea

Hippolyte obliquimanus is a marine shrimp reported from the Caribbean Sea and Brazil. The literature provides indications for morphological variation between populations from those regions and the species has a troubled taxonomic history. The aims of this study were to analyse morphological and genetic variation in the populations of H. obliquimanus from Brazil and the Caribbean Sea and to verify if those might support separation of H. obliquimanus into two or more species. This hypothesis was tested with the analysis of morphological and genetic data (mitochondrial gene 16S and the barcode region Cytochrome Oxidase I). The material analysed was obtained from samples and from loans of zoological collections. The rostrum as well as pereiopods 3, 4, and 5 were the adult morphological characters that showed variation, but this occurred in samples from both regions, Brazil and the Caribbean Sea. The sequences of the 16S gene were identical among all specimens analysed. There was, however, variation among the sequences of the barcoding gene COI (<2.0%); this divergence separated the specimens into two groups (Brazil versus the Caribbean) and these groups did not share haplotypes. In conclusion, specimens from the regions analysed showed both morphological and genetic variation, but these did not support the separation of H. obliquimanus into two or more species.

Is the COI barcoding gene involved in speciation through intergenomic conflict?

We here test the proposition that changes in the barcoding region of COI are commonly involved in speciation through intergenomic conflict. We demonstrate that this is unlikely given that even with incomplete taxon sampling, 78–90% of closely-related animal species have identical COI amino acid sequences. In addition, in those cases where amino acid substitutions between closely related species are observed, the inter- and intra-specific substitution patterns are very similar and/or lack consistent differences in the number, position and type of amino acid change. Overall, we conclude that there is little evidence for a widespread involvement of the barcoding gene in speciation.

Seafood mislabelling: comparisons of two western European case studies assist in defining influencing factors, mechanisms and motives

AbstractThe global seafood industry, influenced by consumer demand, is closely linked to the global fishing industry, which determines the variety of fish available for consumption. The recently revealed issue of seafood mislabelling threatens to weaken this link by removing consumer power to influence patterns of fisheries exploitation through informed choice. Recognizing this, there is an urgent need to go beyond the mere documentation of the phenomenon and learn more about the origins of this problem and the nature of factors influencing its occurrence to develop solutions. In an attempt to understand seafood mislabelling more thoroughly in Europe, 226 cod products were purchased from Ireland and the UK, genetically identified using a DNA barcoding technique (COI barcoding gene), and species identification results were compared against product labels. Cod mislabelling proved more severe in Ireland than in the UK (28.4% vs. 7.4%). Moreover, whereas data show that in Ireland, cheaper species are sold as cod, in the UK, threatened Atlantic cod (Gadus morhua) may be sold as ‘sustainably sourced’ Pacific cod. Considering these countries operate under the same EU policies for seafood traceability and labelling, it is likely that this situation has been influenced by heightened consumer awareness in the UK, which has created an environment where mislabelling is discouraged. In addition to identifying samples, traceability information from packaged cod was used to trace products back to supplying companies. Although inconclusive in determining blame, this exercise has demonstrated that using traceability information can add explanatory power when attempting to determine responsibility for the occurrence of mislabelling.

Cryptic speciation and the circumpolarity debate: A case study on endemic Southern Ocean octopuses using the COI barcode of life

Three hundred and fifty specimens of the endemic Southern Ocean octopus genus Pareledone, were sequenced for the barcoding gene COI. Geographic coverage comprised the South Shetland Islands, the Ross Sea, Adélie Land, George V Land, the Weddell Sea, under the site of the former Larsen B ice shelf, Prydz Bay, the South Orkney Islands and the Amundsen Sea. The greatest number of specimens was captured at the three first-mentioned localities. At least 11 species were represented in the samples and the analyses revealed cryptic species. Six species were found to have extended distributions. Circumpolarity is supported for at least one species. Evidence is presented for a barrier to gene flow to the west of the Antarctic Peninsula, with haplotypes of P. aequipapillae becoming progressively more diverse in a clockwise direction from the South Shetland Islands to the Amundsen Sea. This pattern is akin to that seen in ring species, although we suggest that comparatively warm bottom water acts as a physical barrier preventing completion of the ring.

Unlocking the "Black box": internal female genitalia in Sepsidae (Diptera) evolve fast and are species-specific.

BackgroundThe species-specificity of male genitalia has been well documented in many insect groups and sexual selection has been proposed as the evolutionary force driving the often rapid, morphological divergence. The internal female genitalia, in sharp contrast, remain poorly studied. Here, we present the first comparative study of the internal reproductive system of Sepsidae. We test the species-specificity of the female genitalia by comparing recently diverged sister taxa. We also compare the rate of change in female morphological characters with the rate of fast-evolving, molecular and behavioral characters.ResultsWe describe the ectodermal parts of the female reproductive tract for 41 species representing 21 of the 37 described genera and define 19 morphological characters with discontinuous variation found in eight structures that are part of the reproductive tract. Using a well-resolved molecular phylogeny based on 10 genes, we reconstruct the evolution of these characters across the family [120 steps; Consistency Index (CI): 0.41]. Two structures, in particular, evolve faster than the rest. The first is the ventral receptacle, which is a secondary sperm storage organ. It accounts for more than half of all the evolutionary changes observed (7 characters; 61 steps; CI: 0.46). It is morphologically diverse across genera, can be bi-lobed or multi-chambered (up to 80 chambers), and is strongly sclerotized in one clade. The second structure is the dorsal sclerite, which is present in all sepsids except Orygma luctuosum and Ortalischema albitarse. It is associated with the opening of the spermathecal ducts and is often distinct even among sister species (4 characters; 16 steps; CI: 0.56).ConclusionsWe find the internal female genitalia are diverse in Sepsidae and diagnostic for all species. In particular, fast-evolving structures like the ventral receptacle and dorsal sclerite are likely involved in post-copulatory sexual selection. In comparison to behavioral and molecular data, the female structures are evolving 2/3 as fast as the non-constant third positions of the COI barcoding gene. They display less convergent evolution in characters (CI = 0.54) than the third positions or sepsid mating behavior (CICOI = 0.36; CIBEHAV = 0.45).