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      Inferring the Provenance of an Alien Species with DNA Barcodes: The Neotropical Butterfly Dryas iulia in Thailand

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          Abstract

          The Neotropical butterfly Dryas iulia has been collected from several locations in Thailand and Malaysia since 2007, and has been observed breeding in the wild, using introduced Passiflora foetida as a larval host plant. The butterfly is bred by a butterfly house in Phuket, Thailand, for release at weddings and Buddhist ceremonies, and we hypothesized that this butterfly house was the source of wild, Thai individuals. We compared wing patterns and COI barcodes from two, wild Thai populations with individuals obtained from this butterfly house. All Thai individuals resemble the subspecies D. iulia modesta, and barcodes from wild and captive Thai specimens were identical. This unique, Thai barcode was not found in any of the 30 specimens sampled from the wild in the species' native range, but is most similar to specimens from Costa Rica, where many exporting butterfly farms are located. These data implicate the butterfly house as the source of Thailand's wild D. iulia populations, which are currently so widespread that eradication efforts are unlikely to be successful.

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

          Rudolf Meier, Kwong Shiyang, Gaurav Vaidya … (2006)
          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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            AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics.

            Johan Nylander, James C Wilgenbusch, Dan L Warren … (2008)
            A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation. The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.
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              New M13 vectors for cloning.

              J Messing (1983)
              Article 0 comments Cited 56 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Ben J. Mans: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2014
                Publication date (Electronic): 13 August 2014
                Volume: 9
                Issue: 8
                Electronic Location Identifier: e104076
                Affiliations
                [1 ]Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
                [2 ]Department of Psychology, Hunter College, City University of New York, New York, New York, United States of America
                [3 ]Biology Ph.D. Program, Graduate Center, City University of New York, New York, New York, United States of America
                [4 ]Biology Department, City College of New York, City University of New York, New York, New York, United States of America
                [5 ]High School for Environmental Studies, New York, New York, United States of America
                [6 ]Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, Thailand
                [7 ]Entomology Section, National Museum of the Philippines, Manila, Philippines
                Onderstepoort Veterinary Institute, South Africa
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: DJL. Performed the experiments: NAB AP RMG EZM EWZ. Analyzed the data: NAB DJL. Contributed reagents/materials/analysis tools: DJL WS. Contributed to the writing of the manuscript: NAB DJL.

                Article
                Publisher ID: PONE-D-14-14226
                DOI: 10.1371/journal.pone.0104076
                PMC ID: 4132105
                PubMed ID: 25119899
                SO-VID: 3526aa48-202e-42da-9551-0e60ffdcefce
                Copyright statement: Copyright @ 2014
                License:

                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.

                History
                Date received : 30 March 2014
                Date accepted : 6 July 2014
                Page count
                Pages: 7
                Funding
                National Science Foundation Grant 1120380 to DJL; http://www.nsf.gov/awardsearch/showAward?AWD_ID=1120380. National Science Foundation Grant 0742457 funded NAB; http://www.nsf.gov/awardsearch/showAward?AWD_ID=0742457. Professional Staff Congress of the City University of New York Research Award 60051-40 41 to DJL; https://www.rfcuny.org/rfwebsite/research/content.aspx?catID=1190. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology and life sciences
                Subject: Evolutionary biology
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Subject: Genetics
                Subject: Conservation Genetics
                Subject: Organisms
                Subject: Animals
                Subject: Invertebrates
                Subject: Arthropoda
                Subject: Insects
                Subject: Moths and Butterflies
                Subject: Taxonomy
                Subject: Ecology and Environmental Sciences
                Subject: Conservation Science
                Subject: Species Colonization
                Subject: Invasive Species
                Subject: People and Places
                Subject: Geographical Locations
                Subject: Asia
                Subject: Thailand
                Custom metadata
                Data Availability The authors confirm that all data underlying the findings are fully available without restriction. All DNA sequences are available from the GenBank database (accession numbers GU157119, GU157122–GU157124, GU157126–GU157131, GU333906, GU333908, GU659588, GU659594, GU659619–GU659626, GU659691, GU666775, GU666782, HM416486, JN201279, JN201280, JQ536893, KJ496350–KJ496367). The DNA sequence alignment is available as Supporting Information.

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                Data availability:
                ScienceOpen disciplines: Uncategorized

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