scholarly journals Salix transect of Europe: records of willow-associated weevils (Coleoptera: Curculionoidea) from Greece to Arctic Norway, with insights from DNA barcoding

2020 ◽  
Vol 8 ◽  
Author(s):  
Roy Canty ◽  
Enrico Ruzzier ◽  
Quentin Cronk ◽  
Diana Percy
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Size Variation ◽  
Common Species ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Geographic Clustering ◽  
Site Variation ◽  
The Mean

Curculionid beetles associated with willow (Salix spp.) were surveyed at 42 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). DNA sequence data provide additional verification of identifications and geographic clustering. In all, 73 curculionid species were collected from willows, of which seven were particularly abundant. The most widespread species were: Acalyptus carpini Fabricius, 1793 at 15 sites; Tachyerges stigma Germar, 1821 at 13 sites; Phyllobius oblongus (Linnaeus, 1758) at 11 sites; Phyllobius maculicornis Germar, 1824 at 10 sites; and Archarius salicivorus (Paykull, 1792), Melanapion minimum (Herbst, 1797), and Phyllobius cf. pyri (Linnaeus, 1758) all at nine sites. The mean number of curculionid species collected on willow at each site was 5.5 (range 0-14). Compared to chrysomelids, curculionids were richer in species but the species had relatively low average abundance. Widespread curculionid species appear to have scattered and patchy observed distributions with limited geographical structuring in our data. However, deeper sampling (e.g. over multiple seasons and years), would give a better indication of distribution, and may increase apparent geographical structuring. There is some site-to-site variation in colour in a few taxa, but little notable size variation. DNA barcoding, performed on some of the more common species, provides clear species clusters and definitive separation of the taxonomically more challenging species, as well as some interesting geographic insights. Our northernmost sample of Phyllobius oblongus is unique in clustering with Canadian samples of this species. On the other hand, our samples of Acalyptus carpini cluster with European samples and are distinct from a separate Canadian cluster of this species. We provide the first available DNA sequences for Phyllobius thalassinus Gyllenhal, 1834 (Hungary).

scholarly journals Ecology and seasonality of Pseudo-nitzschia species (Bacillariophyceae) in the northwestern Adriatic Sea over a 30-years period (1988–2020)

2021 ◽  
Vol 22 (3) ◽  
pp. 505
Author(s):  
SONIA GIULIETTI ◽  
TIZIANA ROMAGNOLI ◽  
ALESSANDRA CAMPANELLI ◽  
CECILIA TOTTI ◽  
STEFANO ACCORONI
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Species Complex ◽  
Adriatic Sea ◽  
Sequence Data ◽  
Coastal Station ◽  
Dna Sequence Data ◽  
The Mean ◽  
First Time ◽  
North Western

The ecology and seasonality of Pseudo-nitzschia species and their contribution to phytoplankton community were analysed for the first time at the coastal station of the LTER-Senigallia-Susak transect (north-western Adriatic Sea) from 1988 to 2020. Species composition was addressed using DNA sequence data obtained from 106 monoclonal strains isolated from January 2018 to January 2020. The mean annual cycle of total phytoplankton in the study period (Feb 1988–Jan 2020) showed maximum abundances in winter followed by other peaks in spring and autumn. Diatoms were the main contributors in terms of abundance during the winter and the spring blooms. The autumn peak was due to phytoflagellates and diatoms. In summer phytoflagellates dominated the community, followed by diatoms and dinoflagellates, which in this season reached their annual maximum. Pseudo-nitzschia spp. represented on average 0.4–17.6% of diatom community, but during their blooms they could reach up to up to 90% of the total diatom abundances with 106 cells l-1. By LM, six different taxa were recognized: Pseudo-nitzschia cf. delicatissima and P. cf. pseudodelicatissima were the most abundant, followed by P. cf. fraudulenta, P. pungens, P. multistriata and P. cf. galaxiae. P. cf. fraudulenta and P. pungens were indicator taxa of winter. P. cf. delicatissima and P. cf. pseudodelicatissima were spring and summer taxa, respectively. P. galaxiae showed maximum abundances in autumn. DNA sequences revealed the presence of two species belonging to the ’P. seriata group’ (i.e. P. fraudulenta and P. pungens) and four species belonging to the ‘P. delicatissima group’ (P. calliantha and P. mannii within the P. pseudodelicatissima species complex, and P. delicatissima and P. cf. arenysensis within the P. delicatissima species complex). The presence of several cryptic and pseudo-cryptic species highlights the need to combine LM observations with DNA sequence data when the ecology of Pseudo-nitzschia is investigated. 

scholarly journals EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

2018 ◽  
Author(s):  
Michael Gruenstaeudl ◽  
Yannick Hartmaring
Keyword(s):  
Dna Barcoding ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Software Tool ◽  
Plant Dna ◽  
Dna Sequence Data ◽  
User Friendly ◽  
Common Plant ◽  
Python Package

AbstractBackgroundThe submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding.MethodsA Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called “checklists”) for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled “EMBL2checklists”, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA.ResultsEMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study.DiscussionEMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

A review of the fern genus Pellaea (Pteridaceae) in Australasia

2020 ◽  
Author(s):  
Patrick J. Brownsey ◽  
Daniel J. Ohlsen ◽  
Lara D. Shepherd ◽  
Whitney L. M. Bouma ◽  
Erin L. May ◽  
...  
Keyword(s):  
New Zealand ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Indigenous Species ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Australian Species ◽  
The Status ◽  
Chloroplast Dna Sequences

Five indigenous species of Pellaea in Australasia belong to section Platyloma. Their taxonomic history is outlined, morphological, cytological and genetic evidence for their recognition reviewed, and new morphological and chloroplast DNA-sequence data provided. Australian plants of P. falcata (R.Br.) Fée are diploid and have longer, narrower pinnae than do New Zealand plants previously referred to P. falcata, which are tetraploid. Evidence indicates that P. falcata does not occur in New Zealand, and that collections so-named are P. rotundifolia (G.Forst.) Hook. Chloroplast DNA sequences are uninformative in distinguishing Australian P. falcata from New Zealand P. rotundifolia, but show that Australian P. nana is distinct from both. Sequence data also show that Australian and New Zealand populations of P. calidirupium Brownsey & Lovis are closely related, and that Australian P. paradoxa (R.Br.) Hook. is distinct from other Australian species. Although P. falcata is diploid and P. rotundifolia tetraploid, P. calidirupium, P. nana (Hook.) Bostock and P. paradoxa each contain multiple ploidy levels. Diploid populations of Pellaea species are confined to Australia, and only tetraploids are known in New Zealand. Evolution of the group probably involved hybridisation, autoploidy, alloploidy, and possibly apomixis. Further investigation is required to resolve the status of populations from Mount Maroon, Queensland and the Kermadec Islands.

Cymbidium jiangchengense (Orchidaceae; Epidendroideae; Cymbidiinae), a new species from China: evidence from morphology and DNA sequences

Phytotaxa ◽  
2019 ◽  
Vol 408 (1) ◽  
pp. 77-84
Author(s):  
YING-LI PENG ◽  
ZHUANG ZHOU ◽  
SI-REN LAN ◽  
ZHONG-JIAN LIU
Keyword(s):  
Dna Sequences ◽  
Yunnan Province ◽  
Sequence Data ◽  
Detailed Comparison ◽  
Distinct Species ◽  
Molecular Study ◽  
Orchid Species ◽  
Dna Sequence Data ◽  
Pink Flower ◽  
A New Species

A new orchid species, Cymbidium jiangchengense, from Yunnan Province, China, is described and illustrated. Its distinctiveness is evaluated with morphology and molecular analyses. A detailed comparison between the newly discovered orchid and other members of Cymbidium was performed. The new plant was characterized by stem-like pseudobulbs, narrowly oblong leaves, coriaceous leaves with an acute apex, a 2-flowered inflorescence, a purplish pink flower, narrowly elliptic sepals, petals, a obovate-lanceolate lip with a cordate midlobe, a yellow central callus, and a disc with a trough shape longitudinal lamella from the base extending to the base of the midlobe and a lamellae apex inflated to form two calluses that are not confluent apically. These features distinguish this new orchid from all other known species of Cymbidium. A molecular study based on nuclear ribosomal ITS and plastid matK and rbcL DNA sequence data indicates that C. jiangchengense is a distinct species that sister to C. wadae and a member of section Eburnea, subgenus Cyperorchis.

scholarly journals A likelihood ratio test for species membership based on DNA sequence data

2005 ◽  
Vol 360 (1462) ◽  
pp. 1969-1974 ◽  
Author(s):  
Mikhail V Matz ◽  
Rasmus Nielsen
Keyword(s):  
Dna Barcoding ◽  
Likelihood Ratio ◽  
Likelihood Ratio Test ◽  
Sequence Data ◽  
A Priori ◽  
Real Data ◽  
Ratio Test ◽  
Sequence Variability ◽  
Dna Sequence Data ◽  
Measure Of Uncertainty

DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability.

Association of larvae and adults of Mexican species of Macrelmis (Coleoptera: Elmidae): a preliminary analysis using DNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3361 (1) ◽  
pp. 56-62 ◽  
Author(s):  
JOSEFINA CURIEL ◽  
JUAN J. MORRONE
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Preliminary Analysis ◽  
Sequence Data ◽  
Strong Association ◽  
Life Stages ◽  
Adult Morphology ◽  
Dna Sequence Data ◽  
Mexican Species ◽  
Major Impediment

Insect life stages are known imperfectly in many cases, and classifications are usually based on adult morphology. This isunfortunate as information on other life stages may be useful for biomonitoring. The major impediment to using elmid(Coleoptera) larvae for freshwater biomonitoring is the lack of larval descriptions and illustrations. Reliable molecular proto-cols may be used to associate larvae and adults. After adults of seven species of Mexican Macrelmis were identified morpho-logically, seven larval specimens were associated to them based on two gene fragments: Cox1 and Cob. The phylogeneticanalysis allowed identifying the larval specimens as Macrelmis leonilae, M. scutellaris, M. species 7, M. species 10, and M.species 11. Two species based on adults associated uncertainly with one larva, and one larva did not match with any adult. Adult/larval association in elmids using DNA sequence data seems to be promising in terms of speed and reliability.

A newly recognised species that has been confused with the global polyphagous pest scale insect, Coccus hesperidum Linnaeus (Hemiptera: Coccomorpha: Coccidae)

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 571 ◽  
Author(s):  
YEN-PO LIN ◽  
HIROTAKA TANAKA ◽  
LYN G. COOK
Keyword(s):  
Adult Female ◽  
Dna Sequences ◽  
Sequence Data ◽  
Distinct Species ◽  
Scale Insect ◽  
Scale Insects ◽  
History Museum ◽  
Dna Sequence Data ◽  
Cryptic Species Complex ◽  
Coccus Hesperidum

Coccus hesperidum L. (Hemiptera: Coccomorpha: Coccidae), the type species of the soft scale genus Coccus L., the family Coccidae and the whole of the scale insects (Coccoidea), is a cosmopolitan plant pest. Using DNA sequence data and morphological comparisons, we determine that there is a distinct species that is morphologically very similar to C. hesperidum. Here, we describe the species as Coccus praetermissus Lin & Tanaka sp. n., based on adult female specimens from Australia, Malaysia and Thailand. The adult female of C. praetermissus sp. n. differs from C. hesperidum in having dorsal setae with bluntly rounded tips, whereas they are sharply pointed in C. hesperidum. A detailed description of the newly recognised species is provided, incorporating adult female morphology and DNA sequences from mitochondrial and nuclear loci. Our examination of slides from The Natural History Museum, London, and several Australian institutions indicates that C. praetermissus sp. n. has been confused sometimes with C. hesperidum s. s. These findings have potential relevance to plant biosecurity and quarantine because C. hesperidum is cosmopolitan whereas C. praetermissus sp. n., which is also polyphagous and the two species can share many host plants, currently appears to be more geographically restricted. Additionally, there is deep genetic divergence within C. praetermissus sp. n. that might indicate that it is a cryptic species complex, but wider geographic sampling is required to test this possibility. 

Phylogeny and mtDNA phylogeography of two widespread European pond skater species (Hemiptera-Heteroptera: Gerridae: Gerris Fabricius)

2006 ◽  
Vol 37 (3) ◽  
pp. 335-350 ◽  
Author(s):  
Jakob Damgaard
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Close Relative ◽  
Individual Species ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Central Asian ◽  
Species Groups

AbstractThis study addresses the phylogenetic relationships within and between two widespread Palaearctic pond skater species, Gerris costae and G. thoracicus, by including new DNA sequence data from the Central Asian G. sahlbergi, traditionally assigned as a close relative of G. costae. The results support the assignment of G. costae and G. thoracicus to two individual species groups that are not closely related, but also that G. sahlbergi is nested within G. costae (including subspecies costae, fieberi and poissoni) thus suggesting a new subspecific rank as G. c. sahlbergi. A broad geographical sampling of mitochondrial DNA from populations of G. thoracicus and G. costae (incl. G. c. sahlbergi) shows that the two species are strikingly similar in terms of genetic diversity and lack of geographical substructure, thus adding further evidence for the G. costae group comprising a single, widespread species.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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