Publications

[Hollingsworth, P. M., Forrest, L. L., Spouge, J. L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., Chase, M. W., Cowan, R. S., Erickson, D. L., Fazekas, A. J., Graham, S. W., James, K. E., Kim, K.-J., Kress, W. J., Schneider, H., van AlphenStahl, J. 2009. Proceedings of the National Academy of Sciences. Online Early .]

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions ( spacer, gene, gene, gene, gene, spacer, and spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+ matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

Barcoding Nemo: DNA-Based Identifications for the Ornamental Fish TradeJul 21, 2009 ()

[Steinke, D., Zemlak, T. S., & Hebert, P. D. N. 2009. http://www.plosone.org. 4(7) e6300.]

Background
Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America.

Methodology/Principal Findings
Analysis of the cytochrome c oxidase subunit I (COI) gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%), but nine species included two or three lineages showing much more divergence (2.19–6.52%) and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting.

Conclusions/Significance
Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation.

Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae)Jul 21, 2009 ()

[Valade, R., Kenis, M., Hernandez-Lopez, A., Augustin, S., Mari Mena, N., Magnoux, E., Rougerie, R., Lakatos, F., Roques, A. and Lopez-Vaamonde, C. 2009. Molecular Ecology. Online Early .]

Abstract Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia 25 years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima’s D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared with C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans.

In the dark in a large urban park: DNA barcodes illuminate cryptic and introduced moth speciesJul 09, 2009 ()

[deWaard, J.R., Landry, J.-F., Schmidt, B.C., Derhousoff, J., McLean, J.A. and Humble, L.M. 2009. Biodiversity and Conservation. Online Early .]

To facilitate future assessments of diversity following disturbance events, we conducted a first level inventory of nocturnal Lepidoptera in Stanley Park, Vancouver, Canada. To aid the considerable task, we employed high-throughput DNA barcoding for the rough sorting of all material and for tentative species identifications, where possible. We report the preliminary species list of 190, the detection of four new exotic species (Argyresthia pruniella, Dichelia histrionana, Paraswammerdamia lutarea, and Prays fraxinella), and the potential discovery of two cryptic species. We describe the magnitude of assistance that barcoding presents for faunal inventories, from reducing specialist time to facilitating the detection of native and exotic species at low density.

Multigene phylogeny and DNA barcoding indicate that the Sandwich tern complex (Thalasseus sandvicensis, Laridae, Sternini) comprises two speciesJul 01, 2009 ()

[Efe, M. A., Tavares, E. S., Baker, A. J., & Bonatto, S. L 2009. Molecular Phylogenetics and Evolution. 52(1) 263-267.]

Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria.Jun 16, 2009 ()

[Santamaria, M., Vicario, S., Pappada, G., Scioscia, G., Scazzocchio, C., & Saccone, C. 2009. BMC Bioinformatics. 10(Suppl 6) S15.]

BACKGROUND: A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers.

METHODS: The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries.

RESULTS: After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals.

CONCLUSION: The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.

iBarcode.org: web-based molecular biodiversity analysisJun 16, 2009 ()

[Singer, G., & Hajibabaei, M 2009. BMC Bioinformatics. 10(Suppl 6) S14.]

BACKGROUND: DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets.

RESULTS: Our web-based tools, available at http://www.ibarcode.org, allow the user to manage their barcode datasets, cull out non-unique sequences, identify haplotypes within a species, and examine the within- to between-species divergences. In addition, we provide a number of phylogenetics tools that will allow the user to manipulate phylogenetic trees generated by other popular programs.

CONCLUSION: The use of a web-based portal for barcode analysis is convenient, especially since the WWW is inherently platform-neutral. Indeed, we have even taken care to ensure that our website is usable from handheld devices such as PDAs and smartphones. Although the current set of tools available at iBarcode.org were developed to meet our own analytic needs, we hope that feedback from users will spark the development of future tools. We also welcome user-built modules that can be incorporated into the iBarcode framework.

Migratory Canada geese cause crash of US Airways Flight 1549Jun 08, 2009 ()

[Marra, P. P., Dove, C. J., Dolbeer, R., Dahlan, N. F., Heacker, M., Whatton, J. F, Diggs, N. E, France, C. & Henkes, G. A. 2009. Frontiers in Ecology and the Environment. Online Early .]

In the United States alone, over 7400 bird–aircraft collisions (birdstrikes) were reported in 2007. Most of these strikes occurred during takeoff or landing of the flight, and it is during these flight phases that aircraft experience their highest risk of substantial damage after colliding with birds. Birdstrikes carry enormous potential costs in terms of lives and money. Using feather remains and other tissue samples collected from the engines of US Airways Flight 1549, which crash landed in the Hudson River in New York City on 15 January 2009 after a birdstrike, we apply molecular tools and stable hydrogen isotopes to demonstrate that migratory Canada geese were responsible for the crash. Determining whether the geese involved in this birdstrike event were resident or migratory is essential to the development of management techniques that could reduce the risk of future collisions. Currently, the US civil aviation industry is not required to report birdstrikes, yet information on frequency, timing, and species involved, as well as the geographic origin of the birds, is critical to reducing the number of birdstrikes. Integrating this information with bird migration patterns, bird-detecting radar, and bird dispersal programs at airports can minimize the risk of such collisions in the future.

Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): using a molecular approach to detect arthropod preyJun 01, 2009 ()

[Clare, E. L., Fraser, E. E., Braid, H. E., Fenton, M. B., & Hebert, P. D. N. 2009. Molecular Ecology. 18(11) 2532-2542.]

One of the most difficult interactions to observe in nature is the relationship between a predator and its prey. When direct observations are impossible, we rely on morphological classification of prey remains, although this is particularly challenging among generalist predators whose faeces contain mixed and degraded prey fragments. In this investigation, we used a polymerase chain reaction and sequence-based technique to identify prey fragments in the guano of the generalist insectivore, the eastern red bat (Lasiurus borealis), and evaluate several hypotheses about prey selection and prey defences. The interaction between bats and insects is of significant evolutionary interest because of the adaptive nature of insect hearing against echolocation. However, measuring the successes of predator tactics or particular prey defences is limited because we cannot normally identify these digested prey fragments beyond order or family. Using a molecular approach, we recovered sequences from 89% of the fragments tested, and through comparison to a reference database of sequences, we were able to identify 127 different species of prey. Our results indicate that despite the robust jaws of L. borealis, most prey taxa were softer-bodied Lepidoptera. Surprisingly, more than 60% of the prey species were tympanate, with ears thought to afford protection against these echolocating bats. Moths of the family Arctiidae, which employ multiple defensive strategies, were not detected as a significant dietary component. Our results provide an unprecedented level of detail for the study of predator2013prey relationships in bats and demonstrate the advantages which molecular tools can provide in investigations of complex ecological systems and food-web relationships.

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogenyJun 01, 2009 ()

[Braukmann, T. W. A., Kuzmina, M., & Stefanovic, S. 2009. Current Genetics. 55(3) 323-337.]

The exact phylogenetic position of Gnetales, a small, highly modified group of gymnosperms with an accelerated rate of molecular evolution, is one of the most challenging issues for seed plant systematics. Recent results from entire plastid genome (ptDNA) sequencing revealed the absence of the entire suite of plastid ndh genes in several species of Gnetales and the pine family (Pinaceae) potentially highlighting a major structural feature linking these two groups—concerted loss of all plastid genes for the NADH dehydrogenase complex. However, the precise extent of ndh gene loss in gymnosperms has not been surveyed. Using a slot-blot hybridization method, we probed all 11 ndh genes in 162 species from 70 of 85 gymnosperm genera. We find that all ndh genes are absent across Gnetales and Pinaceae, but not in any other group of gymnosperms. This feature represents either a major synapomorphy for a clade consisting of these two lineages or, less likely, a convergent loss. Our survey substantially extends previous inferences based on more limited sampling and, if the former evolutionary interpretation is correct, it provides additional support for the contentious “gnepine” hypothesis, which places Gnetales as sister to Pinaceae.

A new mouse-eared bat (Mammalia: Chiroptera: Vespertilionidae) from VietnamJun 01, 2009 ()

[Borisenko, A. V., Kruskop, S. V., & Ivanova, N. V. 2009. Russian Journal of Theriology. 7(2) 57-69.]

A new mouse-eared bat (Mammalia: Chiroptera: Vespertilionidae) from the Myotis “siligorensis” species group is being described from the Hon Ba Mountain, ca. 30 km WSW of Nha Trang, Khanh Hoa Province, Vietnam (12.1113° N, 108.953° E, 1250 m ASL), based on a set of morphological and genetic characters. The new species is essentially similar to M. siligorensis alticraniatus, differing in slightly larger size, morphometrics, fine cranial and bacular traits. 12S rDNA demonstrates ca. 2% sequence divergence between the new species and its nearest neighbour, suggesting a history of genetic isolation. Provisional bat survey data from the Bi Doup-Hon Ba massif suggest that, although the new species co-occurs with M. siligorensis in the southern part of the Vietnam Central Highlands area, they are separated by an altitudinal gradient and habitat preferences, the former occupying mature forest at higher elevations and the latter confined to disturbed foothill areas.

On the utility of DNA barcoding for species differentiation among brown macroalgae (Phaeophyceae) including a novel extraction protocolJun 01, 2009 ()

[McDevit, D. C. and G. W. Saunders 2009. Phycological Research. 57(2) 131-141.]

The generation of a species-rich DNA barcode database in combination with rapid and affordable sequencing techniques will dramatically change specimen identification in ecological, biogeographical and taxonomic applications. Though cytochrome c oxidase 1 has been shown to be a useful tool for differentiating some groups of marine algae, its wide application in the Phaeophyceae has yet to be studied. The presence of polymerase chain reaction (PCR) inhibiting compounds in members of the Fucales, Laminariales and Tilopteridales, that are often co-extracted with DNA, has hampered the rapid processing associated with barcode projects. Polyphenolics and polysaccharides are present in concentrations such that DNA extraction methods typically include extensive series of washes, organelle extractions and/or cesium columns. In this paper we examine the utility of cytochrome c oxidase 1 for barcoding the Phaeophyceae and present a method for extracting PCR friendly DNA from brown macroalgae in about 2 h, dramatically reducing the time required from previous methods, some of which take days. This method is easily adapted to a 96 well, high-throughput format and may have applications in other organisms where the presence of similar PCR inhibiting compounds hinders molecular analyses. We extracted DNA from 106 isolates representing 29 species from 20 genera in nine families from five orders of Phaeophyceae. We were able to amplify the barcode marker (cytochrome c oxidase 1) from all samples and a nuclear marker (internal transcribed spacer region) from 54 selected samples. Cytochrome c oxidase 1 was able to differentiate clearly among species, showing within species divergence of 0.00–0.46%, with the exception of one previously studied genus, and between species divergences of greater than 3%.

Morphological and molecular characterization of renal ciliates infecting farmed snails in SpainJun 01, 2009 ()

[Segade, P., Kher, C. P., Lynn, D. H., & Iglesias, R. 2009. Parasitology. 136(7) 771-782.]

Renal infections by parasitic ciliates were studied in adult snails of Helix aspersa aspersa and Helix aspersa maxima collected from 2 mixed rearing system-based heliciculture farms located in Galicia (NW Spain). The occurrence of ciliates was also examined in slugs (Deroceras reticulatum) invading the greenhouses where first growing and fattening of snails is carried out. Histological examinations revealed a severe destruction of the renal epithelium in heavily infected hosts. Three ciliate isolates, one from each host species, were obtained and grown in axenic cultures. Cultured and parasitic ciliates were characterized morphologically and morphometrically. In addition, the encystment behaviour, the occurrence of autogamy, and the sequences of the mitochondrial cytochrome-c oxidase subunit 1 (cox1) and the small subunit ribosomal RNA (SSU rRNA) genes were also studied in the 3 isolates. A polymorphic life cycle involving resting and reproductive cysts, together with the morphological and morphometrical characteristics and the confirmation that autogamy occurs within cysts, demonstrate that our ciliates belong to the species Tetrahymena rostrata (Kahl, 1926) Corliss, 1952. The 3 isolates formed a well-supported clade using both genetic markers, and were clearly separate from the strain ATCC(R) 30770, which has been identified as Tetrahymena rostrata. We argue that our Spanish isolates should be regarded as Tetrahymena rostrata, and that the ATCC isolate should be regarded as a misidentification as neither cytological nor cytogenetical support for its identity has been presented.

High-level genetic diversity but no population structure inferred from nuclear and mitochondrial markers of the peritrichous ciliate Carchesium polypinum in the Grand River basin (North America)May 01, 2009 ()

[Gentekaki, E., & Lynn, D. H. 2009. Appl Environ Microbiol,. 75(10) 3187-3195.]

Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers–ITS1, ITS2, and the hypervariable regions of the large subunit rRNA–and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.

DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approachMay 01, 2009 ()

[Radulovici, A. E., Sainte-Marie, B., & Dufresne, F. 2009. Molecular Ecology Resources. 9(s1) 181-187.]

Marine crustaceans are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some crustaceans. Here we expand the DNA barcode database with a case study involving 80 malacostracan species from the Estuary and Gulf of St Lawrence. DNA sequences for 460 specimens grouped into clusters corresponding to known morphological species in 95% of cases. Genetic distances between species were on average 25 times higher than within species. Intraspecific divergence was high (3.78201313.6%) in specimens belonging to four morphological species, suggesting the occurrence of cryptic species. Moreover, we detected the presence of an invasive amphipod species in the St Lawrence Estuary. This study reconfirms the usefulness of DNA barcoding for the identification of marine crustaceans.

Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British ColumbiaMay 01, 2009 ()

[Saunders, G. W. 2009. Molecular Ecology Resources. 9(s1) 140-150.]

As part of an extensive DNA-based floristic survey of marine macroalgae in Canadian waters, an unexpected sequence for a Gracilaria sp. was generated from British Columbia. Before further molecular analyses and corresponding morphological/anatomical observations this mystery sequence was temporarily entered into our database as Gracilaria BCsp. Continued sampling uncovered this species from four additional locations. A timely collaboration with international colleagues introduced sequences from the invasive Gracilaria vermiculophylla into our cytochrome c oxidase I alignments 2014 these a perfect match to BCsp indicating that this species occurs in British Columbia. A discussion of the origin of this taxon in Canadian waters, whether natural or introduced, is provided.

DNA barcoding reveals overlooked marine fishesMay 01, 2009 ()

[Zemlak, T. S., Ward, R. D., Connell, A. D., Holmes, B. H., & Hebert, P. D. N. 2009. Molecular Ecology Resources. 9(s1) 237-242.]

With more than 15 000 described marine species, fishes are a conspicuous, diverse and increasingly threatened component of marine life. It is generally accepted that most large-bodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence divergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore. A substantial proportion of inshore species showed deep divergences between populations from South African and Australian waters (mean = 5.10%), a pattern which also emerged in a few inshore/offshore species (mean = 0.84%), but not within strictly offshore species (mean = 0.26%). Such deep divergences, detected within certain inshore and inshore/offshore taxa, are typical of divergences between congeneric species rather than between populations of a single species, suggesting that current taxonomic systems substantially underestimate species diversity. We estimate that about one third of the 1000 fish species thought to bridge South African and Australian waters actually represent two taxa.

Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae)May 01, 2009 ()

[Newmaster, S. G., & Ragupathy, S. 2009. Molecular Ecology Resources,. 9(s1) 172-180.]

Acacia species are quite difficult to differentiate using morphological characters. Routine identification of Acacia samples is important in order to distinguish invasive species from rare species or those of economic importance, particularly in the forest industry. The genus Acacia is quite abundant and diverse comprising approximately 1355 species, which is currently divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species). It would be prudent to utilize DNA barcoding in the accurate and efficient identification of acacias. The objective of this research is to test barcoding in discriminating multiple populations among a sister-species complex in pantropical Acacia subg. Acacia, across three continents. Based on previous research, we chose three cpDNA regions (rbcL, trnH-psbA and matK). Our results show that all three regions (rbcL, matK and trnH-psbA) can distinguish and support the newly proposed genera of Vachellia Wight & Arn. from Acacia Mill., discriminate sister species within either genera and differentiate biogeographical patterns among populations from India, Africa and Australia. A morphometric analysis confirmed the cryptic nature of these sister species and the limitations of a classification based on phenetic data. These results support the claim that DNA barcoding is a powerful tool for taxonomy and biogeography with utility for identifying cryptic species, biogeograhic patterns and resolving classifications at the rank of genera and species.

A new cleptoparasitic Lasioglossum (Hymenoptera, Halictidae) from AfricaMay 01, 2009 ()

[Gibbs, J. 2009. Journal of Hymenoptera Research. 18 74-79.]

Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approachMay 01, 2009 ()

[Wong, E. H.-K., Shivji, M. S., & Hanner, R. H. 2009. Molecular Ecology Resources. 9(s1) 243-256.]

Shark fisheries worldwide are mostly unmanaged, but the burgeoning shark fin industry in the last few decades has made monitoring catch and trade of these animals critical. As a tool for molecular species identification, DNA barcoding offers significant potential. However, the genetic distance-based approach towards species identification employed by the Barcode of Life Data Systems may oftentimes lack the specificity needed for regulatory or legal applications that require unambiguous identification results. This is because such specificity is not typically realized by anything less than a 100% match of the query sequence to an entry in the reference database using genetic distance. Although various divergence thresholds have been proposed to define acceptable levels of intraspecific variation, enough exceptions exist to cast reasonable doubt on many less than exact matches using a distance-based approach for the identification of unknowns. An alternative approach relies on the identification of discrete molecular characters that can be used to unambiguously diagnose species. The objective of this study was to assess the performance differences between these competing approaches by examining more than 1000 DNA barcodes representing nearly 20% of all known elasmobranch species. Our results demonstrate that a character-based, nucleotide diagnostic (ND) approach to barcode identification is feasible and also provides novel insights into the structure of haplotype diversity among closely related species of sharks. Considerations for the use of NDs in applied fields are also explored.

Combining DNA barcoding and morphological analysis to identify specialist floral parasites (Lepidoptera: Coleophoridae: Momphinae: Mompha)May 01, 2009 ()

[Emery, V. J., Landry, J.-F., & Eckert, C. G. 2009. Molecular Ecology Resources. 9(s1) 217-223.]

Close interactions between insects and plants have played a major role in the evolution of both these diverse groups of organisms. Studying these interactions, however, can be difficult because many insects, especially parasites, impinge most strongly on plants during larval stages when they are morphologically difficult to identify, and many belong to diverse groups for which most species remain undescribed. We used DNA barcoding to identify nondescript lepidopteran larvae that regularly parasitize flower buds of the coastal dune endemic Camissoniopsis cheiranthifolia (Onagraceae). We obtained cytochrome oxidase 1 mitochondrial DNA sequences from 201 parasite specimens from across the host geographical range. The Barcode of Life Database Identification System combined with Bayesian analysis grouped all 15 parasite haplotypes in a distinct, monophyletic clade within the genus Mompha (Lepidoptera: Coleophoridae: Momphinae), a group known to be host specialists on plants of the Onagraceae. Species identity and phylogenetic affinities within Mompha could not be confirmed because few barcode sequences exist from this diverse and poorly known group of moths. However, morphological analysis, including detailed dissection of genitalia for a subsample of 23 reared adults and comparison with known species of Mompha, also indicated that the larvae parasitizing C. cheiranthifolia constitute a distinct and undescribed species within this genus. Knowing that floral parasitism of C. cheiranthifolia involves a single, putatively host-specific microlepidopteran greatly facilitates formulating and testing hypotheses concerning how floral parasitism has promoted the evolution of striking floral diversity within this species. More generally, DNA barcoding combined with morphological analysis can greatly hasten identification of problematic specimens and enhance our understanding of the diversity, ecology and evolution of plant2013insect interactions.

DNA barcode accumulation curves for understudied taxa and areasMay 01, 2009 ()

[Smith, M. A., Fernandez-Triana, J., Roughley, R., & Hebert, P. D. N. 2009. Molecular Ecology Resources. 9(s1) 208-216.]

Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment 2014 parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha-taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.

http://www3.interscience.wiley.com/cgi-bin/fulltext/122342777/HTMLSTART

Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae)May 01, 2009 ()

[Rivera, J., & Currie, D. C. 2009. Molecular Ecology Resources. 9(s1) 224-236.]

DNA barcoding has gained increased recognition as a molecular tool for species identification in various groups of organisms. In this preliminary study, we tested the efficacy of a 615-bp fragment of the cytochrome c oxidase I (COI) as a DNA barcode in the medically important family Simuliidae, or black flies. A total of 65 (25%) morphologically distinct species and sibling species in species complexes of the 255 recognized Nearctic black fly species were used to create a preliminary barcode profile for the family. Genetic divergence among congeners averaged 14.93% (range 2.83201315.33%), whereas intraspecific genetic divergence between morphologically distinct species averaged 0.72% (range 020133.84%). DNA barcodes correctly identified nearly 100% of the morphologically distinct species (87% of the total sampled taxa), whereas in species complexes (13% of the sampled taxa) maximum values of divergence were comparatively higher (max. 4.5820136.5%), indicating cryptic diversity. The existence of sibling species in Prosimulium travisi and P. neomacropyga was also demonstrated, thus confirming previous cytological evidence about the existence of such cryptic diversity in these two taxa. We conclude that DNA barcoding is an effective method for species identification and discovery of cryptic diversity in black flies.

DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studiesMay 01, 2009 ()

[Sheffield, C. S., Hebert, P. D. N., Kevan, P. G., & Packer, L. 2009. Molecular Ecology Resources. 9(s1) 196-207.]

DNA barcoding has been evaluated for many animal taxa and is now advocated as a reliable and rapid means for species-level identification. The coming-to-light of this identification tool is timely as we are now facing perhaps the greatest rate of species loss in recent millennia. This study contributes to an ever-increasing number of published accounts of DNA barcoding successfully and accurately distinguishing animal taxa, in this instance, the bee fauna of Nova Scotia, Canada. Most members of this well-known fauna were resolved with particular clarity; the average intraspecific divergence was less than 0.5%, and COI sequences from over 75% of the province’s species are now in the Barcodes of Life Data System. DNA barcoding also revealed some surprises within this fauna, including the possible recognition of two undescribed genetically unique species, one in the genus Ceratina (subgenus Zadontomerus), the second in the genus Andrena (subgenus Larandrena); both are presently receiving further taxonomic study. In addition, DNA barcoding has allowed sex-associations among two pairs of cleptoparasitic species. The resulting utility of DNA barcoding for ecological studies of bee communities is discussed.

Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?May 01, 2009 ()

[Fazekas, A. J., Kesanakurti, P. R., Burgess, K. S., Percy, D. M., Graham, S. W., Barrett, S. C. H., Newmaster, S. G., Hajibabaei, M., & Husband, B. C. 2009. Molecular Ecology Resources. 9(s1) 130-139.]

The ability to discriminate between species using barcoding loci has proved more difficult in plants than animals, raising the possibility that plant species boundaries are less well defined. Here, we review a selection of published barcoding data sets to compare species discrimination in plants vs. animals. Although the use of different genetic markers, analytical methods and depths of taxon sampling may complicate comparisons, our results using common metrics demonstrate that the number of species supported as monophyletic using barcoding markers is higher in animals (> 90%) than plants (~70%), even after controlling for the amount of parsimony-informative information per species. This suggests that more than a simple lack of variability limits species discrimination in plants. Both animal and plant species pairs have variable size gaps between intra- and interspecific genetic distances, but animal species tend to have larger gaps than plants, even in relatively densely sampled genera. An analysis of 12 plant genera suggests that hybridization contributes significantly to variation in genetic discontinuity in plants. Barcoding success may be improved in some plant groups by careful choice of markers and appropriate sampling; however, overall fine-scale species discrimination in plants relative to animals may be inherently more difficult because of greater levels of gene-tree paraphyly.

Multiple copies of cytochrome oxidase 1 in species of the fungal genus FusariumMay 01, 2009 ()

[Gilmore, S. R., Grafenhan, T., Louis-Seize, G., & Seifert, K. A. 2009. Molecular Ecology Resources. 9(s1) 90-98.]

Using data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1-based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences.

DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea)May 01, 2009 ()

[Foottit, R. G., Maw, H. E. L., Havill, N. P., Ahern, R. G., & Montgomery, M. E. 2009. Molecular Ecology Resources,. 9(s1) 188-195.]

The Adelgidae are relatively small, cryptic insects, exhibiting complex life cycles with parthenogenetic reproduction. Due to these characteristics, the taxonomy of the group is problematic. Here, we test the effectiveness of the standard 658-bp barcode fragment from the 5′-end of the mitochondrial cytochrome c oxidase 1 gene (COI) in differentiating among 17 species of Adelgidae, in associating life-cycle stages, and in assessing patterns of geographical variation in selected species. Species of Adelgidae are well-differentiated by DNA barcodes, enabling the identification of different morphological forms, immature stages and individuals on different hosts and at different periods of the life cycle. DNA barcodes have uncovered cryptic diversity within taxa and, in other cases, a lack of sequence divergence in species pairs previously separated by life-cycle characteristics, indicating a need for further taxonomic analysis.

Countering criticisms of single mitochondrial DNA gene barcoding in birdsMay 01, 2009 ()

[Baker, A. J., Tavares, E. S., & Elbourne, R. F 2009. Molecular Ecology Resources. 9(s1) 257-268.]

General criticisms of a single mtDNA gene barcodes include failure to identify newly evolved species, use of species-delimitation thresholds, effects of selective sweeps and chance occurrence of reciprocal monophyly within species, inability to deal with hybridization and incomplete lineage sorting, and superiority of multiple genes in species identification. We address these criticisms in birds because most species are known and thus provide an ideal test data set, and we argue with selected examples that with the exception of thresholds these criticisms are not problematic for avian taxonomy. Even closely related sister species of birds have distinctive COI barcodes, but it is not possible to universally apply distance thresholds based on ratios of within-species and among-species variation. Instead, more rigorous methods of species delimitation should be favoured using coalescent-based techniques that include tests of chance reciprocal monophyly, and times of lineage separation and sequence divergence. Incomplete lineage sorting is also easily detected with DNA barcodes, and usually at a younger time frame than a more slowly evolving nuclear gene. Where DNA barcodes detect divergent reciprocally monophyletic lineages, the COI sequences can be combined with multiple nuclear genes to distinguish between speciation or population subdivision arising from high female philopatry or regional selective sweeps. Although selective sweeps are increasingly invoked to explain patterns of shallow within-species coalescences in COI gene trees, caution is warranted in this conjecture because of limited sampling of individuals and the reduced power to detect additional mtDNA haplotypes with one gene.

Biological agent detection technologiesMay 01, 2009 ()

[Jakupciak, J. P., & Colwell, R. R 2009. Molecular Ecology Resources. 9(s1) 51-57.]

The challenge for first responders, physicians in the emergency room, public health personnel, as well as for food manufacturers, distributors and retailers is accurate and reliable identification of pathogenic agents and their corresponding diseases. This is the weakest point in biological agent detection capability today. There is intense research for new molecular detection technologies that could be used for very accurate detection of pathogens that would be a concern to first responders. These include the need for sensors for multiple applications as varied as understanding the ecology of pathogenic micro-organisms, forensics, environmental sampling for detect-to-treat applications, biological sensors for ‘detect to warn’ in infrastructure protection, responses to reports of ‘suspicious powders’, and customs and borders enforcement, to cite a few examples. The benefits of accurate detection include saving millions of dollars annually by reducing disruption of the workforce and the national economy and improving delivery of correct countermeasures to those who are most in need of the information to provide protective and/or response measures.

DNA barcoding and the mediocrity of morphologyMay 01, 2009 ()

[Packer, L., Gibbs, J., Sheffield, C., & Hanner, R. 2009. Molecular Ecology Resources. 9(s1) 42-50.]

A small but vocal community of critics has questioned the epistemological value of DNA barcoding by suggesting that either it ‘cannot work’ for the identification or discovery of species or that it ignores the ‘richness’ inherent in traditional approaches. We re-examine these arguments through a comparison of DNA barcoding and morphological taxonomy in terms of their accuracy and diversity of characters employed. We conclude that morphology often does not work and that it is often nowhere near as ‘rich’ as has been argued. Morphology is particularly poor in numerous important situations, such as the association of larvae with adults and discrimination among cryptic species. The vehemence of some of the criticisms is surprising given that morphology alone is known to be inadequate to the task of species-level identification in many instances.

Express barcodes: racing from specimen to identificationMay 01, 2009 ()

[Ivanova, N. V., Borisenko, A. V., & Hebert, P. D. N. 2009. Molecular Ecology Resources. 9(s1) 35-41.]

Although devices combining microfluidic and advanced sequencing technologies promise a future where one can generate a DNA barcode in minutes, current analytical regimes typically involve workflows that extend over 2 days. Here we describe simple protocols enabling the advance from a specimen to barcode-based identification in less than 2 h. The protocols use frozen or lyophilized reagents that can be prepackaged into ‘kits’ and support barcode analysis across the animal kingdom. The analytical procedure allows 5 min for DNA extraction, 25 min for polymerase chain reaction amplification of the barcode region, 25 min for cycle-sequencing, 10 min for cleanup, 45 min for capillary sequencing and 5 min for trace file analysis to complete DNA-based identification. This study involved the comparison of varied DNA preservation and extraction methods, and evaluated Taq polymerases with high processivity and resistance to inhibitors.

Efficient algorithms for the discovery of DNA oligonucleotide barcodes from sequence databasesMay 01, 2009 ()

[Zahariev, M., Dahl, V., Chen, W., & Levesque, C. A. 2009. Molecular Ecology Resources. 9(s1) 58-64.]

Efficient design of barcode oligonucleotides can lead to significant cost reductions in the manufacturing of DNA arrays. Previous methods are based on either a preliminary alignment, which reduces their efficiency for intron-rich regions, or on a brute force approach, not feasible for large-scale problems or on data structures with very poor performance in the worst case. One of the algorithms we propose uses ‘oligonucleotide sorting’ for the discovery of oligonucleotide barcodes of given sizes, with good asymptotic performance. Specific barcode oligonucleotides with at least one base difference from other sequences in a database are found for each individual sequence. With another algorithm, specific oligonucleotides can also be found for groups or clades in the database, which have 100% homology for all oligonucleotide sequences within the group or clade while having differences with the rest of the data. By re-organizing the sequences/groups in the database, oligonucleotides for different hierarchical levels can be found. The oligonucleotides or polymorphism locations identified as species or clade specific by the new algorithm are refined and screened further for hybridization thermodynamic properties with third party software.

Barcoding diatoms: Is there a good marker?May 01, 2009 ()

[Moniz, M. B. J., & Kaczmarska, I. 2009. Molecular Ecology Resources. 9(s1) 65-74.]

The promise of DNA barcoding is based on a small DNA fragment divergence coinciding with biological species separation. Here we evaluated the performance of three markers as diatom barcodes, the small ribosomal subunit (1600 bp), a 5′ end fragment of cytochrome c oxidase subunit 1 (430 bp), and the second internal transcribed spacer region combined with the 5.8S gene (5.8S + ITS-2, 3002013400 bp). Forty-four sequences per marker representing 28 species from all diatom classes were analysed. Sequence alignment of the three genetic markers and uncorrected genetic distances (P) were calculated at the intra- and heterospecific level. All three markers correctly separated the species examined and had advantages which contribute to their feasibility as a DNA barcode. Small ribosomal subunit had the largest GenBank data set, its success rate in amplification and sequencing was assumed to be the highest of all three and was readily aligned. However, it required a long fragment to recover divergence sufficient for species separation and small genetic distances increased the potential for misidentifications. Cytochrome c oxidase subunit 1 demonstrated a substantial heterospecific divergence level and was also readily alignable, but it showed very low amplification and sequencing success rates with currently existing primers. 5.8S + ITS-2 was amplified and sequenced with high success rate and was the most variable of the three markers, but its secondary structure was needed to aid in alignment. However, since it has been recently suggested that ITS-2 may provide insight into sexual compatibility, this marker offers an additional advantage. We therefore propose that the 5.8S + ITS-2 fragment is the best candidate as a diatom DNA barcode.

DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern IndiaMay 01, 2009 ()

[Ragupathy, S., Newmaster, S. G., Murugesan, M., & Balasubramaniam, V. 2009. Molecular Ecology Resources. 9(s1) 164-171.]

Our research brought together traditional aboriginal knowledge (TK) and scientific knowledge (SK) to explore the relationship between scientific and aboriginal systems of botanical classification and the corresponding valorization(s) of biological diversity in the Western Ghats of southern India. We worked with two aboriginal cultures namely ‘Irulas’ and ‘Malasars’ of the Nilgiri Biosphere Reserve with an objective of evaluating the ability of different knowledge systems (SK and TK) to distinguish grass species belonging to the genus Tripogon, and assess the ability of DNA barcoding to discriminate a new cryptic species ‘Tripogon cope’ as deciphered by the hill tribes. We discovered that the aboriginal informants identified a common ethnotaxa ‘Sunai pul’, which is a cryptic species of grass not recognized by the SK classification.’sunai pul’ is very important to both aboriginal cultures with ritualistic and economic utility. Morphometric analysis confirms the cryptic nature of this new species, which was validated using DNA barcoding. DNA barcode regions matK and trnH-psbA showed distinct sequence variations among the closely related ethnotaxa. Given the cryptic nature of ethnotaxa, we propose that a DNA barcode may be a reliable tool to identify ethnotaxa. We have initiated further studies in other cultures to develop theoretically sophisticated insights concerning the encounter between ‘local’ and ‘scientific’ approaches to the use of biodiversity knowledge. Furthermore, the research will add to a unifying global effort to speed up the documentation and understanding of the planet’s natural diversity, while simultaneously respecting the cultural heterogeneity as a vital component of biological diversity.

Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminthsMay 01, 2009 ()

[Moszczynska, A., Locke, S. A., McLaughlin, J. D., Marcogliese, D. J., & Crease, T. J. 2009. Molecular Ecology Resources. 9(s1) 75-82.]

The phylum Platyhelminthes is a diverse group of flatworms that includes parasites with serious impacts on human health, animal husbandry, aquaculture and wildlife management. Here we present degenerate primers for the barcode region of the mitochondrial cytochrome c oxidase I (COI) gene in flatworms. Although amplicons were obtained from a wide taxonomic range in the Cestoda and Trematoda, COI fragments from many taxa in these classes did not amplify. Primers specific to trematodes in the family Diplostomidae were also developed. Amplification success was much higher with diplostomid-specific primers and sequences were obtained from 504 of 585 specimens of Diplostomum and Tylodelphys. Sequences from the barcode region resolved all specimens to the species level, with mean divergence between congeners of 19% (3.9201325%). Because many of our specimens were small, we initially amplified part of the nuclear small subunit ribosomal (r) RNA gene to evaluate the quality and quantity of DNA in our specimens. Short sequences (~380 nt) of this gene were recovered from most specimens and can be used to distinguish specimens at the family level and often the generic level. We suggest that rRNA genes could be used to screen samples of completely unknown taxonomy, after which specific COI primers could be used to obtain species-level identifications.

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus PenicilliumMay 01, 2009 ()

[Chen, W., Seifert, K. A., & Levesque, C. A. 2009. Molecular Ecology Resources. 9(s1) 114-129.]

We developed a COX1 barcode oligonucleotide array based on 358 sequences, including 58 known and two new species of Penicillium subgenus Penicillium, and 12 allied species. The array was robotically spotted at near microarray density on membranes. Species and clade-specific oligonucleotides were selected using the computer programs SigOli and Array Designer. Robotic spotting allowed 768 spots with duplicate sets of perfect match and the corresponding mismatch and positive control oligonucleotides, to be printed on 2 × 6 cm2 nylon membranes. The array was validated with hybridizations between the array and digoxigenin (DIG)-labelled COX1 polymerase chain reaction amplicons from 70 pure DNA samples, and directly from environmental samples (cheese and plants) without culturing. DNA hybridization conditions were optimized, but undesired cross-reactions were detected frequently, reflecting the relatively high sequence similarity of the COX1 gene among Penicillium species. Approximately 60% of the perfect match oligonucleotides were rejected because of low specificity and 76 delivered useful group-specific or species-specific reactions and could be used for detecting certain species of Penicillium in environmental samples. In practice, the presence of weak signals on arrays exposed to amplicons from environmental samples, which could have represented weak detections or weak cross reactions, made interpretation difficult for over half of the oligonucleotides. DNA regions with very few single nucleotide polymorphisms or lacking insertions/deletions among closely related species are not ideal for oligonucleotide-based diagnostics, and supplementing the COX1-based array with oligonucleotides derived from additional genes would result in a more robust hierarchical identification system.

The front-end logistics of DNA barcoding: challenges and prospectsMay 01, 2009 ()

[Borisenko, A. V., Sones, J. E., & Hebert, P. D. N. 2009. Molecular Ecology Resources. 9(s1) 27-34.]

Building a global library of DNA barcodes will require efficient logistics of pre-laboratory specimen processing and seamless interfacing with molecular protocols. If not addressed properly, the task of aggregating specimens may become the biggest bottleneck in the analytical chain. Three years of experience in developing a collection management system to facilitate high-throughput DNA barcoding have allowed the Canadian Centre for DNA Barcoding to recognize and resolve the most common logistical obstacles. Dealing with these challenges on a larger scale will be an important step towards building a solid collection-based foundation for the international DNA barcoding effort.

Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)May 01, 2009 ()

[Starr, J. R., Naczi, R. F. C., & Chouinard, B. N. 2009. Molecular Ecology Resources. 9(s1) 151-163.]

We investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH-psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best-known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., 2265 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH-psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50201360% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0201313%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH-psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system. Although identification rates in this study are low, they can be significantly improved by a regional approach to barcoding.

Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity.May 01, 2009 ()

[Janzen, D. H., Hallwachs, W., Blandin, P., Burns, J. M., Cadiou, J.-M., Chacon, I., et al. 2009. Molecular Ecology Resources. 9(s1) 1-26.]

Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today’s Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 020132000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding 2014 the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species 2014 was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to ‘variation’ or thought to be insignificant for species-level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.

Evaluation of mitochondrial genes as DNA barcode for BasidiomycotaMay 01, 2009 ()

[Vialle, A., Feau, N., Allaire, M., Didukh, M., Martin, F., Moncalvo, J.-M., & Hamelin, R. C. 2009. Molecular Ecology Resources. 9(s1) 99-113.]

Our study evaluated in silico the potential of 14 mitochondrial genes encoding the subunits of the respiratory chain complexes, including cytochrome c oxidase I (CO1), as Basidiomycota DNA barcode. Fifteen complete and partial mitochondrial genomes were recovered and characterized in this study. Mitochondrial genes showed high values of molecular divergence, indicating a potential for the resolution of lower-level relationships. However, numerous introns occurred in CO1 as well as in six other genes, potentially interfering with polymerase chain reaction amplification. Considering these results and given the minimal length of 600-bp that is optimal for a fungal barcode, the genes encoding for the ATPase subunit 6, the cytochrome oxidase subunit 3 and the NADH dehydrogenase subunit 6 have the most promising characteristics for DNA barcoding among the mitochondrial genes studied. However, biological validation on two fungal data sets indicated that no single mitochondrial gene gave a better taxonomic resolution than the ITS, the region already widely used in fungal taxonomy.

Progress towards DNA barcoding of fungiMay 01, 2009 ()

[Seifert, K. A. 2009. Molecular Ecology Resources. 9(s1) 83-89.]

The use of DNA sequences for identifying fungi and fungus-like organisms predates the DNA barcoding movement by at least 10 years. A brief overview of the mycological shift from phenotypic to molecular taxonomy is provided. Exploration of the animal barcode marker, cytochrome oxidase 1, by Canadian mycologists has been fruitful for some fungi, but intron issues and lack of resolution in other taxa prevent its universal application. The momentum established by 15 years of research on the fungal nuclear ribosomal internal transcribed spacer (ITS) sequences will lead to a proposal to the Consortium for the Barcode of Life on the adoption of this marker as the fungal barcode. Existing mycological research networks should facilitate the rapid development of DNA barcoding of fungi once the marker issue is settled. Some available online fungal identification databases are briefly described.

Molecular Ecology Resources: Special Issue on Barcoding LifeApr 23, 2009 ()

[http://www3.interscience.wiley.com/journal/122342767/issue 2009. Molecular Ecology Resources. Volume 9 Issue S1 1-268.]

The Canadian Barcode of Life Network has made a substantial contribution to the literature on DNA barcoding with the new release of  a  special issue of Molecular Ecology Resources that is entirely dedicated to barcoding. This volume stems from our Network’s  Scientific Symposium held at the ROM last spring and represents a major milestone for our national network.

This collection of 27 papers is accessible online: http://www3.interscience.wiley.com/journal/122342767/issue

Public Health Response to Puffer Fish (Tetrodotoxin) Poisoning from Mislabeled ProductApr 01, 2009 ()

[Cohen, N. J., Deeds, J. R., Wong, E. S., Hanner, R. J., Yancy, H. F., White, K. D., Thompson, T. M., Wahl, M., Pham, T. D., Guichard, F. M., Huh, I., Austion, C., Dizikes, G., & Gerber, S. I. 2009. Journal of Food Protection. 72(4) 810-817.]

Tetrodotoxin is a neurotoxin that occurs in select species of the family Tetraodontidae (puffer fish). It causes paralysis and potentially death if ingested in sufficient quantities. In 2007, two individuals developed symptoms consistent with tetrodotoxin poisoning after ingesting home-cooked puffer fish purchased in Chicago. Both the Chicago retailer and the California supplier denied having sold or imported puffer fish but claimed the product was monkfish. However, genetic analysis and visual inspection determined that the ingested fish and others from the implicated lot retrieved from the supplier belonged to the family Tetraodontidae. Tetrodotoxin was detected at high levels in both remnants of the ingested meal and fish retrieved from the implicated lot. The investigation led to a voluntary recall of monkfish distributed by the supplier in three states and placement of the supplier on the U.S. Food and Drug Administration’s Import Alert for species misbranding. This case of tetrodotoxin poisoning highlights the need for continued stringent regulation of puffer fish importation by the U.S. Food and Drug Administration, education of the public regarding the dangers of puffer fish consumption, and raising awareness among medical providers of the diagnosis and management of foodborne toxin ingestions and the need for reporting to public health agencies.

A botanical renaissance: state-of-the-art DNA bar coding facilitates an Automated Identification Technology system for plantsApr 01, 2009 ()

[Newmaster, S. G., Ragupathy, S., & Janovec, J. 2009. International Journal of Computer Applications in Technology. 35(1) 50-60.]

Traditional taxonomic practices are insufficient on their own to cope with the growing need for accurate identifications. The recent development of DNA barcoding has been applied to plants. The next step is the development of a high-throughput Automated Identification Technology (AIT) system. Our research indicates that the efficacy of an AIT system equates with savings in time and funding. Given the potential interconnectivity of web-based applications, we suggest an AIT system for plants that uses several existing systems and suggest several applications where AIT could serve as a tool for biologists and for society at large.

Population genetic structure of the salmon louse, Lepeophtheirus salmonis (Krøyer) on wild and farmed salmonids around the Pacific coast of CanadaMar 09, 2009 ()

[Boulding, E. G., deWaard, J. R., Ang, K. P., & Hebert, P. D. N. 2009. Aquaculture Research. 40(8) 973-979.]

Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae)Mar 01, 2009 ()

[Gibbs, J. 2009. Zootaxa. 2032 1-38.]

An integrative taxonomic approach that utilizes the DNA barcode region of cytochrome c oxidase subunit 1 in conjunction with traditional morphological approaches identifies five distinct species previously recognized as Lasioglossum (Dialictus) tegulare (Robertson). Differences in DNA sequences and congruent, albeit minor, morphological variation support separation of L. tegulare into five species. Unique nucleotide substitution patterns for each species allows for character-based diagnostics using DNA barcodes. The names L. ellisiae (Sandhouse) and L. lepidii (Graenicher) are removed from synonymy. Two new species, L. puteulanum Gibbs sp. n. and L. carlinvillense Gibbs sp. n., are described. A key is provided, which permits the identification of both males and females. The utility of the DNA barcode region as part of an integrative taxonomic framework is discussed.

Letters to the EditorMar 01, 2009 ()

[Wilson, John J., Floyd, R., Hanner, R. H., & Castle, D. 2009. Isis. 100(1) 117.]

DNA Barcodes and Insect BiodiversityMar 01, 2009 ()

[Floyd, R., Wilson, J. J., & Hebert, P. D. N. 2009. In R. G. Foottit & P. H. Adler (Eds.), Insect Biodiversity: Science and Society. Oxford, UK: Blackwell Publishing. 417-431.]

Fungal pathogen (mis-) identifications: A case study with DNA barcodes on Melampsora rusts of aspen and white poplarFeb 26, 2009 ()

[Feau, N., Vialle, A., Allaire, M., Tanguay, P., Joly, D. L., Frey, P., Callan, B. E., & Hamelin, R. C 2009. Mycological Research. 113(6-7) 713-724.]

Wide variation and overlap in morphological characters have led to confusion in species identification within the fungal rust genus Melampsora. The Melampsora species with uredinial–telial stages on white poplar and aspens are especially prone to misidentification. This group includes the Melampsora populnea species complex and the highly destructive pine twisting rust, Melampsora pinitorqua, which alternates between hosts in Populus section Populus and Pinus. Our objective was to compare morphologically based identification to genetic material extracted from Melampsora species pathogenic to aspen and white poplar. We compared morphometric traits and DNA barcodes obtained from internal transcribed spacer (ITS), large ribosomal RNA subunit (28S), and mitochondrial cytochrome oxidase 1 (CO1) sequences to delimit within this taxonomically difficult group. Eight different Melampsora species were initially defined based on host specificity and morphometric data. DNA barcodes were then overlaid on these initial species definitions. The DNA barcodes, specifically those defined on ITS and 28S sequences, provided a highly accurate means of identifying and resolving Melampsora taxa. We highlighted species misidentification in specimens from Canadian herbaria related to either Melampsora medusae f. sp. tremuloidae or Melampsora aecidioides. Finally, we evidenced that the north-American species found on Populus alba, M. aecidioides is closely related but distinct from the four species of the M. populnea complex (Melampsora larici-tremulae, Melampsora magnusiana, Melampsora pinitorqua, and Melampsora rostrupii) found in Eurasia.

How Many Loci Does it Take to DNA Barcode a Crocus?Feb 25, 2009 ()

[Seberg, O., & Petersen, G. 2009. PLoS ONE. 4(2) e4598.]

Background

DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species.

Methodology and Principal Findings

Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will – as is the case in crocus – undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached – even in a taxonomic context.

Conclusions/Significance

The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.

Probing Evolutionary Patterns in Neotropical Birds through DNA BarcodesFeb 05, 2009 ()

[Kerr, K. C. R., Lijtmaer, D. A., Barreira, A. S., Hebert, P. D. N., & Tubaro, P. L. 2009. PLoS ONE. 4(2) e4379.]

Background

The Neotropical avifauna is more diverse than that of any other biogeographic region, but our understanding of patterns of regional divergence is limited. Critical examination of this issue is currently constrained by the limited genetic information available. This study begins to address this gap by assembling a library of mitochondrial COI sequences, or DNA barcodes, for Argentinian birds and comparing their patterns of genetic diversity to those of North American birds.

Methodology and Principal Findings

Five hundred Argentinian species were examined, making this the first major examination of DNA barcodes for South American birds. Our results indicate that most southern Neotropical bird species show deep sequence divergence from their nearest-neighbour, corroborating that the high diversity of this fauna is not based on an elevated incidence of young species radiations. Although species ages appear similar in temperate North and South American avifaunas, patterns of regional divergence are more complex in the Neotropics, suggesting that the high diversity of the Neotropical avifauna has been fueled by greater opportunities for regional divergence. Deep genetic splits were observed in at least 21 species, though distribution patterns of these lineages were variable. The lack of shared polymorphisms in species, even in species with less than 0.5M years of reproductive isolation, further suggests that selective sweeps could regularly excise ancestral mitochondrial polymorphisms.

Conclusions

These findings confirm the efficacy of species delimitation in birds via DNA barcodes, even when tested on a global scale. Further, they demonstrate how large libraries of a standardized gene region provide insight into evolutionary processes.

DNA barcoding for ecologistsFeb 01, 2009 (pdf)

[Valentini, A., Pompanon, F. and P. Taberlet 2009. Trends in Ecology and Evolution. 24(2) 110-117.]

DNA barcoding  taxon identification using a standardized DNA region  has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism’s remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.

The campaign to DNA barcode all fishes, FISH-BOLJan 29, 2009 ()

[Ward, R. D., Hanner, R., & Hebert, P. D. N. 2009. Journal of Fish Biology. 74(2) 329-356.]

FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.

Species identification of North American guinea worms (Nematoda: Dracunculus) with DNA barcodingJan 28, 2009 ()

[Elsasser, S. C., Floyd, R., Hebert, P. D. N., & Schulte-Hostedde, A. I. 2009. Molecular Ecology Resources. Online Early .]

Dracunculus insignis is a nematode parasite that infects the subcutaneous tissues of mammals such as raccoon (Procyon lotor), mink (Neovison vison) and fisher (Martes pennanti). D. lutrae, a morphologically similar species, has only been recovered from the otter (Lontra canadensis). Species identification of these two North American guinea worms has only been achieved by morphology of males and host identity. As a result, where only female specimens are present, accurate identifications are not possible. To date, specimens recovered from otter have been assumed to be D. lutrae, while those from all other hosts are assumed to be D. insignis. This study uses DNA barcoding to differentiate between these two North American dracunculoids. Our results show that D. insignis is a ‘true’ generalist, showing little sequence divergence regardless of host association, although our studies did validate its occurrence in a new host 2014 the otter. Interestingly, specimens of the host specialist, D. lutrae, showed some sequence divergence, although it was low. The finding of D. insignis in otter substantiates the need to supplement morphology-based methods in providing species identifications for certain dracunculoids.

Identification of shark and ray fins using DNA barcodingJan 14, 2009 ()

[Holmes, B. H., Steinke, D., & Ward, R. D. 2009. Fisheries Research. 95(2-3) 280-288.]

Fisheries managers and scientists worldwide are struggling with a lack of basic information for many shark and ray species. One factor hampering the data collection is inaccurate identification of many chondrichthyan species and their body parts. Morphologically similar species, and specimens which are poorly preserved or have had key diagnostic features removed, can be difficult to identify. This study examined DNA barcoding as a method to identify shark species from dried fins, confiscated from a vessel fishing illegally in Australian waters. 211 left pectoral fins were examined. 18 either did not provide a sequenceable product or yielded a microbial sequence, while 193 fins (91.5%) provided a chondrichthyan sequence. All of these could be matched to reference specimens in a DNA barcode database, and so were able to be identified. 27 species were detected, 20 species of sharks and seven species of rays The most abundant species (22% of fins) was Carcharhinus dussumieri. Many of these species are listed on the World Conservation Union (IUCN) Red List and include one, Anoyxpristis cuspidata (3%), rated as critically endangered. Fishing authorities can use DNA barcoding to gather data on which chondrichthyan species are targeted by illegal fishers, information that will greatly assist in management and conservation.

Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda)Jan 07, 2009 ()

[Ferri, E., Barbuto, M., Bain, O., Galimberti, A., Uni, S., Guerrero, R. A., Ferte, H., Bandi, C., Martin, C., & Casiraghi, M. 2009. Front Zool. 6(1) 1.]

ABSTRACT: BACKGROUND: We compared here the suitability and efficacy of traditional morphological approach and DNA barcoding to distinguish filarioid nematodes species (Nematoda, Spirurida). A reliable and rapid taxonomic identification of these parasites is the basis for a correct diagnosis of important and widespread parasitic diseases. The performance of DNA barcoding with different parameters was compared measuring the strength of correlation between morphological and molecular identification approaches. Molecular distance estimation was performed with two different mitochondrial markers (coxI and 12S rDNA) and different combinations of data handling were compared in order to provide a stronger tool for easy identification of filarioid worms. RESULTS: DNA barcoding and morphology based identification of filarioid nematodes revealed high coherence. Despite both coxI and 12S rDNA allow to reach high-quality performances, only coxI revealed to be manageable. Both alignment algorithm, gaps treatment, and the criteria used to define the threshold value were found to affect the performance of DNA barcoding with 12S rDNA marker. Using coxI and a defined level of nucleotide divergence to delimit species boundaries, DNA barcoding can also be used to infer potential new species. CONCLUSIONS: An integrated approach allows to reach a higher discrimination power. The results clearly show where DNA-based and morphological identifications are consistent, and where they are not. The coherence between DNA-based and morphological identification for almost all the species examined in our work is very strong. We propose DNA barcoding as a reliable, consistent, and democratic tool for species discrimination in routine identification of parasitic nematodes.

Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodesJan 01, 2009 ()

[Valdez-Moreno, M., Ivanova, N. V., Elías-Gutiérrez, M., Contreras-Balderas, S., & Hebert, P. D. N. 2009. Journal of Fish Biology. 74(2) 377-402.]

The freshwater fish fauna of Mexico and Guatemala is exceptionally diverse with >600 species, many endemic. In this study, patterns of sequence divergence were analysed in representatives of this fauna using cytochrome c oxidase subunit 1 (COI) DNA barcodes for 61 species in 36 genera. The average divergence among conspecific individuals was 0·45%, while congeneric taxa showed 5·1% divergence. Three species of Poblana, each occupying a different crater lake in the arid regions of Central Mexico, have had a controversial taxonomic history but are usually regarded as endemics to a single lake. They possess identical COI barcodes, suggesting a very recent history of isolation. Representatives of the Cichlidae, a complex and poorly understood family, were well discriminated by barcodes. Many species of Characidae seem to be young, with low divergence values (<2%), but nevertheless, clear barcode clusters were apparent in the Bramocharax2013Astyanax complex. The symbranchid, Opisthernon aenigmaticum, has been regarded as a single species ranging from Guatemala to Mexico, but it includes two deeply divergent barcode lineages, one a possible new endemic species. Aside from these special cases, the results confirm that DNA barcodes will be highly effective in discriminating freshwater fishes from Central America and that a comprehensive analysis will provide new important insights for understanding diversity of this fauna.

Rapid Range Expansion of the Wool-Carder Bee, Anthidium manicatum (Linnaeus) (Hymenoptera: Megachilidae), in North AmericaJan 01, 2009 ()

[Gibbs, J. & Sheffield, C. S. 2009. Journal of the Kansas Entomological Society. 82(1) 21-29.]

Anthidium manicatum (L.) is an adventive species of European origin first recorded in North America in the late 1960’s; from that point until 2001 its range on the continent was restricted to the northeast central USA and central Canada (Ontario, more recently Que´bec). In 2005, this species was reported from Nova Scotia, a rapid and wide increase in its distribution. In this paper, we document a similar rapid spread of A. manicatum into western North America, including British Columbia and Idaho, and discuss the potential risks of this species in eastern Canada. In addition, the potential of DNA barcoding as a rapid and reliable means of recognizing adventive bee species is advocated.

The Use of Mean Instead of Smallest Interspecific Distances Exaggerates the Size of the "Barcoding Gap" and Leads to MisidentificationJan 01, 2009 ()

[Meier, R., Zhang, G., & Ali, F. 2009. Systematic Biology. 57(5) 809-813.]

Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genesDec 01, 2008 ()

[Chantangsi, C., & Lynn, D. H. 2008. Mol Phylogenet Evol. 49(3) 979-987.]

Details of the phylogenetic relationships among tetrahymenine ciliates remain unresolved despite a rich history of investigation with nuclear gene sequences and other characters. We examined all available species of Tetrahymena and three other tetrahymenine ciliates, and inferred their phylogenetic relationships using nearly complete mitochondrial cytochrome c oxidase subunit 1 (cox1) and small subunit (SSU) rRNA gene sequences. The inferred phylogenies showed the genus Tetrahymena to be monophyletic. The three "classical" morphology-and-ecology-based groupings are paraphyletic. The SSUrRNA phylogeny confirmed the previously established australis and borealis groupings, and nine ribosets. However, these nine ribosets were not well supported. Using cox1 gene, the deduced phylogenies based on this gene revealed 12 well supported groupings, called coxisets, which mostly corresponded to the nine ribosets. This study demonstrated the utility of cox1 for resolving the recent phylogeny of Tetrahymena, whereas the SSU rRNA gene provided resolution of deeper phylogenetic relationships within the genus.

Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakesDec 01, 2008 ()

[Meixner, M. J., Luter, C., Eckert, C., Itskovich, V., Janussen, D., von Rintelen, T., Bohne, A. V., Meixner, J. M., and Hess, W. R. 2008. Mol Phylogenet Evol. 45(3) 875-886.]

Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.

DNA Barcoding of Lepetodrilus Limpets Reveals Cryptic SpeciesDec 01, 2008 ()

[Johnson, S. B., Warén, A., & Vrijenhoek, R. C. 2008. Journal of Shellfish Research. 27(1) 43-51.]

Lepetodrilid limpets are common inhabitants of deep-sea hydrothermal vents worldwide, but the frequent occurrence of morphologically cryptic species makes their identification very difficult. To facilitate these identifications, we provide DNA barcodes based on 1,000 bp of cytochrome-c-oxidase subunit I (COI), for 20 taxa within the genus Lepetodrilus. The method was also used to identify lepetodrilids that were found living on vent decapods. A preliminary phylogenetic analysis resolved relationships among members of several cryptic species complexes; however, COI sequences alone were unable to resolve higher-level systematic relationships caused by saturation of synonymous nucleotide substitutions.

Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selectionDec 01, 2008 ()

[Albu, M., Min, X. J., Hickey, D., & Golding, B. 2008. Mol Biol Evol. 25(12) 2521-2524.]

The relative rates of nucleotide substitution at synonymous and nonsynonymous sites within protein-coding regions have been widely used to infer the action of natural selection from comparative sequence data. It is known, however, that mutational and repair biases can affect rates of evolution at both synonymous and nonsynonymous sites. More importantly, it is also known that synonymous sites are particularly prone to the effects of nucleotide bias. This means that nucleotide biases may affect the calculated ratio of substitution rates at synonymous and nonsynonymous sites. Using a large data set of animal mitochondrial sequences, we demonstrate that this is, in fact, the case. Highly biased nucleotide sequences are characterized by significantly elevated dN/dS ratios, but only when the nucleotide frequencies are not taken into account. When the analysis is repeated taking the nucleotide frequencies at each codon position into account, such elevated ratios disappear. These results suggest that the recently reported differences in dN/dS ratios between vertebrate and invertebrate mitochondrial sequences could be explained by variations in mitochondrial nucleotide frequencies rather than the effects of positive Darwinian selection.

Integrating DNA barcoding into the mycological sciencesDec 01, 2008 ()

[Seifert, K. A. 2008. Persoonia. 21 162-166.]