118 research outputs found
Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia ‘pulex’ in New Zealand fresh waters
No full textWe used a DNA barcoding approach to identify specimens of the Daphnia pulex complex occurring in New Zealand lakes, documenting the establishment of non-indigenous North American Daphnia 'pulex'. Morphological delineation of species in this complex is problematic due to a lack of good morphological traits to distinguish the species, as there is a relatively high degree of morphological stasis within the group through evolutionary time. Accordingly, genetic analyses were used to determine the specific identity and likely geographic origin of this species. Morphologically, individuals most closely resembled Daphnia pulicaria or Daphnia pulex sensu lato, which cannot be separated morphologically. Furthermore, each of these taxa comprises separate species in North America and Europe, despite carrying the same names. We identified individuals using a 658 bp nucleotide portion of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) as North American Daphnia 'pulex', being distinct from European Daphnia pulex sensu stricto and D. pulicaria from Europe or North America. Cellulose allozyme electrophoresis was used to confirm that individuals were not hybrids with D. pulicaria. North American Daphnia 'pulex' in New Zealand were first recorded in New Zealand from South Island lakes that are popular for overseas recreational fishers, indicating a possible source of introduction for this species (e.g. on/in fishing gear). Our study provides an additional example of how genetic techniques can be used for the accurate identification of non-indigenous taxa, particularly when morphological species determination is not possible. The growth of global databases such as GenBank and Barcode of Life Datasystems (BOLD) will further enhance this identification capacity
Neotropical Bats: Estimating Species Diversity with DNA Barcodes
No full textPMCID: PMC3144236This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The first-generation Daphnia magna linkage map
No full textAbstract Background Daphnia magna is a well-established model species in ecotoxicology, ecology and evolution. Several new genomics tools are presently under development for this species; among them, a linkage map is a first requirement for estimating the genetic background of phenotypic traits in quantitative trait loci (QTL) studies and is also very useful in assembling the genome. It also enables comparative studies between D. magna and D. pulex, for which a linkage map already exists. Results Here we describe the first genetic linkage map of D. magna. We generated 214 F2 (intercross) clonal lines as the foundation of the linkage analysis. The linkage map itself is based on 109 microsatellite markers, which produced ten major linkage groups ranging in size from 31.1 cM to 288.5 cM. The total size of this linkage map extends to 1211.6 Kosambi cM, and the average interval for the markers within linkage groups is 15.1 cM. The F2 clones can be used to map QTLs for traits that differ between the parental clones. We successfully mapped the location of two loci with infertility alleles, one inherited from the paternal clone (Iinb1) and the other from the maternal clone (Xinb3). Conclusions The D. magna linkage map presented here provides extensive coverage of the genome and a given density of markers that enable us to detect QTLs of moderate to strong effects. It is similar in size to the linkage map of D. pulex.</p
Australian Sphingidae – DNA Barcodes Challenge Current Species Boundaries and Distributions
No full text© 2014 Rougerie et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
Testing use of mitochondrial COI sequences for the identification and phylogenetic analysis of New Zealand caddisflies (Trichoptera)
No full textWe tested the hypothesis that cytochrome c oxidase subunit 1 (COI) sequences would successfully discriminate recognised species of New Zealand caddisflies. We further examined whether phylogenetic analyses, based on the COI locus, could recover currently recognised superfamilies and suborders. COI sequences were obtained from 105 individuals representing 61 species and all 16 families of Trichoptera known from New Zealand. No sequence sharing was observed between members of different species, and congeneric species showed from 2.3 to 19.5% divergence. Sequence divergence among members of a species was typically low (mean = 0.7%; range 0.0–8.5%), but two species showed intraspecific divergences in excess of 2%. Phylogenetic reconstructions based on COI were largely congruent with previous conclusions based on morphology, although the sequence data did not support placement of the purse-cased caddisflies (Hydroptilidae) within the uncased caddisflies, and, in particular, the Rhyacophiloidea. We conclude that sequence variation in the COI gene locus is an effective tool for the identification of New Zealand caddisfly species, and can provide preliminary phylogenetic inferences. Further research is needed to ascertain the significance of the few instances of high intra-specific divergence and to determine if any instances of sequence sharing will be detected with larger sample sizes
Cryptic Species? Patterns of Maternal and Paternal Gene Flow in Eight Neotropical Bats
No full textPMCID: PMC3144194This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Wolbachia and DNA barcoding insects: patterns, potential and problems
No full textWolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region
Contributions to the study of the Holarctic\ua0fauna of Microgastrinae (Hymenoptera,\ua0Braconidae). I. Introduction and first results of transatlantic\ua0comparisons
No full textVolume: 37Start Page: 61End Page: 7
Singing from the Grave: DNA from a 180 Year Old Type Specimen Confirms the Identity of Chrysoperla carnea (Stephens)
No full textCopyright: © 2015 Price et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy
No full textBackground: The sulfide-rich Frasassi caves in central Italy contain a rare example of a freshwater ecosystem
supported entirely by chemoautotrophy. Niphargus ictus, the sole amphipod species previously reported from this locality, was recently shown to host the first known case of a freshwater chemoautotrophic symbiosis. Since the
habitat of N. ictus is highly fragmented and is comprised of streams and lakes with various sulfide concentrations,
we conducted a detailed study to examine the potential genetic diversity of this species within Frasassi.
Results: By sequencing one nuclear (ITS) and two mitochondrial (COI and 12S) regions, we show that four partially sympatric Niphargus clades are present in Frasassi. Morphological and behavioral data obtained for three of these clades are perfectly congruent with this molecular delineation and make it possible to distinguish them in the field. Phylogenetic analyses of 28S ribosomal DNA sequences reveal that, among the four clades, only two are closely related to each other. Moreover, these four clades occupy distinct niches that seem to be related to the
chemical properties and flow regimes of the various water bodies within Frasassi.
Conclusions: Our results suggest that four distinct Niphargus species are present in Frasassi and that they
originated from three or four independent invasions of the cave system. At least two among the four species harbor Thiothrix epibionts, which paves the way for further studies of the specificity and evolutionary history of this
symbiosis
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