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      Molecular taxonomy of Tomares hairstreaks (Lepidoptera, Lycaenidae, Theclinae)

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      Deutsche Entomologische Zeitschrift
      Pensoft Publishers

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          Abstract

          Tomares hairstreaks comprise about 10 species distributed from Europe and North Africa to Central Asia. The taxonomy of the genus is hampered by the absence of diagnostic characters by which specimens can be unambiguously assigned to species. Our investigation of morphology and DNA barcode variations within and between Tomares species shows that while well-defined species (T. ballus, T. mauritanicus, T. callimachus, T. desinens and T. fedtschenkoi) diverge, poorly characterized taxa (T. nogelii, T. nesimachus, T. dobrogensis, T. romanovi and T. telemachus) show very little to no differentiation in mtDNA. We reinstate Tomares callimachus spp. hafis (Kollar, 1849) as a valid subspecies (stat. rev.) and propose taxa telemachus Zhdanko, 2000 and uighurica Koçak, Seven & Kemal, 2000 as synonyms of T. romanovi and T. nogelii nogelii respectively (syn. nov.). We relegate Polyommatus epiphania Boisduval, 1848, recently revived as a valid subspecies of T. callimachus, back to synonymy under the latter, and reconsider the status of T. nogelii dobrogensis (Caradja, 1895) in the light of new molecular data. We use a nuclear gene (EF-1α) in addition to COI barcodes to reconstruct the phylogeny of the group.

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          The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

          CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.
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            A universal DNA mini-barcode for biodiversity analysis

            Background The goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identification in several animal groups. It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental samples (where universal primers are needed). Results We used a bioinformatics analysis using all CO1 barcode sequences from GenBank and calculated the probability of having species-specific barcodes for varied size fragments. This analysis established the potential of much smaller fragments, mini-barcodes, for identifying unknown specimens. We then developed a universal primer set for the amplification of mini-barcodes. We further successfully tested the utility of this primer set on a comprehensive set of taxa from all major eukaryotic groups as well as archival specimens. Conclusion In this study we address the important issue of minimum amount of sequence information required for identifying species in DNA barcoding. We establish a novel approach based on a much shorter barcode sequence and demonstrate its effectiveness in archival specimens. This approach will significantly broaden the application of DNA barcoding in biodiversity studies.
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              Critical factors for assembling a high volume of DNA barcodes.

              Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.
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                Author and article information

                Journal
                Deutsche Entomologische Zeitschrift
                DEZ
                Pensoft Publishers
                1860-1324
                1435-1951
                May 05 2020
                May 05 2020
                : 67
                : 1
                : 19-33
                Article
                10.3897/dez.67.50252
                7cb90c4b-8ad9-4bf1-90d0-78079e77dd1c
                © 2020

                http://creativecommons.org/licenses/by/4.0/

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