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      The Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications

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          Abstract

          Bactrocera carambolae is one of the approximately 100 sibling species of the Bactrocera dorsalis complex and considered to be very closely related to B. dorsalis. Due to their high morphological similarity and overlapping distribution, as well as to their economic impact and quarantine status, the development of reliable markers for species delimitation between the two taxa is of great importance. Here we present the complete mitochondrial genome of B. carambolae sourced from its native range in Malaysia and its invaded territory in Suriname. The mitogenome of B. carambolae presents the typical organization of an insect mitochondrion. Comparisons of the analyzed B. carambolae sequences to all available complete mitochondrial sequences of B. dorsalis revealed several species-specific polymorphic sites. Phylogenetic analysis based on Bactrocera mitogenomes supports that B. carambolae is a differentiated taxon though closely related to B. dorsalis. The present complete mitochondrial sequences of B. carambolae could be used, in the frame of Integrative Taxonomy, for species discrimination and resolution of the phylogenetic relationships within this taxonomically challenging complex, which would facilitate the application of species-specific population suppression strategies, such as the sterile insect technique.

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          DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

          DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.
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            Isolation of plant DNA from fesh tissue

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              Integrative taxonomy: a multisource approach to exploring biodiversity.

              Good alpha taxonomy is central to biology. On the basis of a survey of arthropod studies that used multiple disciplines for species delimitation, we evaluated the performance of single disciplines. All included disciplines had a considerable failure rate. Rigor in species delimitation can thus be increased when several disciplines chosen for complementarity are used. We present a flexible procedure and stopping rule for integrative taxonomy that uses the information from different disciplines separately. Disagreement among disciplines over the number and demarcation of species is resolved by elucidating and invoking evolutionary explanations for disagreement. With the identification of further promising study organisms and of new questions for in-depth analysis, evolutionary biology should profit from integrative taxonomy. An important rationale is clarity in researcher bias in the decision-making process. The success of integrative taxonomy will further increase through methodological progress, taxonomic training of evolutionary biologists, and balanced resource allocation.
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                Author and article information

                Journal
                Insects
                Insects
                insects
                Insects
                MDPI
                2075-4450
                28 November 2019
                December 2019
                : 10
                : 12
                : 429
                Affiliations
                [1 ]Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; aksyllas@ 123456bio.auth.gr (A.S.); giwta_gout@ 123456windowslive.com (P.G.); alkiszisiadis@ 123456gmail.com (G.-A.Z.); theodoki@ 123456bio.auth.gr (T.K.); mitsajohn@ 123456gmail.com (D.P.); sentigeo@ 123456yahoo.gr (G.S.)
                [2 ]Consultant, retired from Ministry of Agriculture, Animal Husbandry and Fisheries, Carambola Fruit Fly Project, Damboentong 282, Tijgerkreek, Saramacca, Suriname; aliesmuller@ 123456yahoo.com
                [3 ]Center for Insect Systematics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; slwee@ 123456ukm.edu.my
                [4 ]Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; antoniosaugustinos@ 123456gmail.com (A.A.A.); K.Bourtzis@ 123456iaea.org (K.B.)
                [5 ]Biology Department, University of Patras, 26504 Patras, Greece; zacharop@ 123456upatras.gr
                Author notes
                [* ]Correspondence: edrosopo@ 123456bio.auth.gr ; Tel.: +30-2310-998291; Fax: +30-2310-998333
                [†]

                Present address: Department of Plant Protection, Institute of Industrial and Forage Crops, Hellenic Agricultural Organization—Demeter, 26442 Patras, Greece.

                Author information
                https://orcid.org/0000-0001-9805-0572
                https://orcid.org/0000-0003-3682-6077
                Article
                insects-10-00429
                10.3390/insects10120429
                6955806
                31795125
                3a289ead-e54f-414f-ae5a-d07d44a4c2ac
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 11 November 2019
                : 21 November 2019
                Categories
                Article

                bactrocera dorsalis species complex,carambola fruit fly,mitogenome,nucleotide polymorphisms,species delimitation,sterile insect technique

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