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Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: an Example from Queensland, Australia

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Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: an Example from Queensland, Australia diversity Article Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: An Example from Queensland, Australia Craig M. Costion 1,*, Andrew J. Lowe 2,†, Maurizio Rossetto 3, Robert M. Kooyman 3,4, Martin F. Breed 2, Andrew Ford 5 and Darren M. Crayn 6,† 1 Botany Department, National Museum of Natural History, MRC 166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA 2 School of Biological Sciences and the Environment Institute, University of Adelaide, Adelaide 5005, Australia; [email protected] (A.J.L.); [email protected] (M.F.B.) 3 National Herbarium of NSW, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney 2000, Australia; [email protected] 4 Department of Biological Sciences, Macquarie University, Sydney 2109, Australia; [email protected] 5 CSIRO Land and Water, Tropical Forest Research Centre, Atherton 4883, Australia; [email protected] 6 Australian Tropical Herbarium, James Cook University, Smithfield 4878, Australia; [email protected] * Correspondence: [email protected]; Tel.: +1-202-633-0920 (ext. 123); Fax: +1-202-786-2563 † These authors contributed equally to this work. Academic Editor: Michael Wink Received: 19 October 2015; Accepted: 24 February 2016; Published: 29 February 2016 Abstract: A foundation for a DNA barcode reference library for the tropical plants of Australia is presented here. A total of 1572 DNA barcode sequences are compiled from 848 tropical Queensland species. The dataset represents 35% of the total flora of Queensland’s Wet Tropics Bioregion, 57% of its tree species and 28% of the shrub species. For approximately half of the sampled species, we investigated the occurrence of infraspecific molecular variation in DNA barcode loci rbcLa, matK, and the trnH-psbA intergenic spacer region across previously recognized biogeographic barriers. We found preliminary support for the notion that DNA barcode reference libraries can be used as a tool for inferring biogeographic patterns at regional scales. It is expected that this dataset will find applications in taxonomic, ecological, and applied conservation research. Keywords: biogeography; wet tropics; rbcLa; matK; trnH-psbA intergenic spacer 1. Introduction Tropical rain forests present unique challenges to identifying plant species. They are characteristically diverse, with an area as small as two hectares potentially containing 300+ vascular woody species of trees, shrubs, and lianas [1]. Many of these species can be extremely rare and/or poorly known [2] and often their most diagnostic characters for identification (e.g., leaves, fruit and flowers) occur high in the canopy out of sight and reach. In many cases fruits and/or flowers are required for accurate identification, which can hinder progress on identification of tropical species in remote localities for years or even decades. This combination of factors renders identification of species in tropical forests to be characteristically slow and dependent on trained experts in taxonomy. Taxonomy, the scientific discipline of identifying and assigning names to species, may be one of the world’s oldest professions, yet today it is undoubtedly an uncommon trade. Although there has been much recent discussion about the discipline of taxonomy being in a state of decline [3], a recent Diversity 2016, 8, 5; doi:10.3390/d8010005 www.mdpi.com/journal/diversity Diversity 2016, 8, 5 2 of 9 paper [4] suggested the opposite is true. Between 1864 and 2010, the number of authors describing new species, articles describing new species and total new species described in the zoological record has increased. This may be attributed to the development of new research methods and approaches or the “publication landscape” changing as science publications have become more interdisciplinary in nature. This trend, plus the rise of the international DNA barcoding initiative, are shifting the ways new speciesDiversity are 2016 discovered, 8, 5 and expanding the traditional horizons of the discipline of taxonomy.2 of 9 The International Barcode of Life Project (iBOL) was established in 2009 and uses standardized portions of a been much recent discussion about the discipline of taxonomy being in a state of decline [3], a recent species genomepaper [4] to suggested identify the species, opposite with is true. the Between aim to aid1864 traditional and 2010, the taxonomy number of andauthors species describing identification. Now speciesnew species, can be articles identified describing from new plant species leaf and fragments total new and species cambium described [ 5in], the roots zoological [6], herbal record medicine preparationshas increased. bought inThis stores may [be7], attributed meat bought to the de atvelopment the market of new [8], research fecal remains methods of and animals approaches [9], and even from digestedor the “publication plant tissues landscape” inside changing the guts as of science insects publications [10]. These have new become and more innovative interdisciplinary methods hold in nature. This trend, plus the rise of the international DNA barcoding initiative, are shifting the much promise for addressing some of the challenges of identifying plant species in the tropics and are ways new species are discovered and expanding the traditional horizons of the discipline of expectedtaxonomy. to accelerate The theInternational discovery Barcode of new of species.Life Project (iBOL) was established in 2009 and uses Thestandardized primary mission portions of ofiBOL a species is to genome provide to identify a platform species, for with the the construction aim to aid traditional of a global DNA barcode referencetaxonomy and library species of identification. species, the Now Barcode species of can Life beData identified Systems from plant (BOLD) leaf fragments [11], and and to promote increasedcambium geographic [5], roots and [6], taxonomic herbal medicine coverage preparations of the speciesbought in currently stores [7], represented.meat bought at BOLDthe market is an online [8], fecal remains of animals [9], and even from digested plant tissues inside the guts of insects [10]. resourceThese developed new and by innovative the Canadian methods Centre hold much for prom DNAise Barcodingfor addressing (CCDB), some of whichthe challenges stores of the DNA barcode records,identifying all plant supporting species in tracethe tropics file sequenceand are expe datacted to as accelerate well as thethe discovery data on theof new voucher species.collections for each DNAThe sample. primary BOLD mission also of iBOL enables is to globalprovide communitya platform for access the construction to the data of a with global online DNA tools for visualization,barcode species reference validation, library of species, and analysis. the Barcode It is of now Life aData central Systems data (BOLD) repository [11], and and to promote informatics hub increased geographic and taxonomic coverage of the species currently represented. BOLD is an for DNA barcoding projects worldwide. online resource developed by the Canadian Centre for DNA Barcoding (CCDB), which stores the ThisDNA project barcode aims records, to construct all supporting a DNA trace barcodefile sequence library data as for well the as tropicalthe data on flora the voucher of Australia in collaborationcollections with iBOLfor each and DNA the sample. CCDB. BOLD As a startingalso enab pointles global we community present analyses access to of the 1572 data DNA with barcodes from 848online species tools from for visualization, Queensland. species In validation, addition and to providinganalysis. It is anow broad a central coverage data repository of the and species that occur in theinformatics region, hub the for project DNA barcoding sampled projects multiple worldwide. individuals per species for approximately half of This project aims to construct a DNA barcode library for the tropical flora of Australia in the sampledcollaboration species with (473) iBOL to and investigate the CCDB. theAs a occurrence starting point ofwe infraspecific present analyses molecular of 1572 DNA variation barcodes in DNA barcode loci.from 848 species from Queensland. In addition to providing a broad coverage of the species that occur in Thethe Australian region, the stateproject ofsampled Queensland multiple individual is the world’ss per species sixth for largestapproxim sub-nationalately half of the politicalsampled region, spanningspecies more (473) than to investigate 1,850,000 the km occurrence2. Over of halfinfraspecific of Queensland molecular variation lies in in theDNA southern barcode loci. tropics. Great The Australian state of Queensland is the world’s sixth largest sub-national political region, diversity of landscapes and climates has allowed a large number of plant species to evolve. The 2014 spanning more than 1,850,000 km2. Over half of Queensland lies in the southern tropics. Great Census ofdiversity the Queensland of landscapes Flora and climates [12] lists has 14,174allowed nativea large number plant species,of plant species making to evolve. Queensland The 2014 the most species richCensus state of ofthe Australia,Queensland plusFlora it[12] contains lists 14,174 three native out plant of thespecies, 12 majormaking AustralianQueensland the centres most of plant endemismspecies [13]. rich This state project of Australia, focuses plus on it contains plants three occurring out of the in 12 the major tropical Australian northern centres part of plant of the state, specificallyendemism
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