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      Mapping Biodiversity and Setting Conservation Priorities for SE Queensland’s Rainforests Using DNA Barcoding

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          Abstract

          Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

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          Opposing effects of competitive exclusion on the phylogenetic structure of communities.

          Though many processes are involved in determining which species coexist and assemble into communities, competition is among the best studied. One hypothesis about competition's contribution to community assembly is that more closely related species are less likely to coexist. Though empirical evidence for this hypothesis is mixed, it remains a common assumption in certain phylogenetic approaches for inferring the effects of environmental filtering and competitive exclusion. Here, we relate modern coexistence theory to phylogenetic community assembly approaches to refine expectations for how species relatedness influences the outcome of competition. We argue that two types of species differences determine competitive exclusion with opposing effects on relatedness patterns. Importantly, this means that competition can sometimes eliminate more different and less related taxa, even when the traits underlying the relevant species differences are phylogenetically conserved. Our argument leads to a reinterpretation of the assembly processes inferred from community phylogenetic structure.
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            Use of DNA barcodes to identify flowering plants.

            Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.
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              The matrix matters: effective isolation in fragmented landscapes.

              Traditional approaches to the study of fragmented landscapes invoke an island-ocean model and assume that the nonhabitat matrix surrounding remnant patches is uniform. Patch isolation, a crucial parameter to the predictions of island biogeography and metapopulation theories, is measured by distance alone. To test whether the type of interpatch matrix can contribute significantly to patch isolation, I conducted a mark-recapture study on a butterfly community inhabiting meadows in a naturally patchy landscape. I used maximum likelihood to estimate the relative resistances of the two major matrix types (willow thicket and conifer forest) to butterfly movement between meadow patches. For four of the six butterfly taxa (subfamilies or tribes) studied, conifer was 3-12 times more resistant than willow. For the two remaining taxa (the most vagile and least vagile in the community), resistance estimates for willow and conifer were not significantly different, indicating that responses to matrix differ even among closely related species. These results suggest that the surrounding matrix can significantly influence the "effective isolation" of habitat patches, rendering them more or less isolated than simple distance or classic models would indicate. Modification of the matrix may provide opportunities for reducing patch isolation and thus the extinction risk of populations in fragmented landscapes.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                24 March 2015
                2015
                : 10
                : 3
                : e0122164
                Affiliations
                [1 ]Genecology Research Center, Faculty of Science, Health, Education, and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
                [2 ]Queensland Herbarium, Queensland Department of Science, Information Technology, Innovation and the Arts, Brisbane Botanic Gardens, Toowong, Queensland, Australia
                [3 ]Australian Museum, Sydney, Australia
                [4 ]National Museum of Natural History, Smithsonian Institution Washington D.C., United States of America
                The New York Botanical Garden, UNITED STATES
                Author notes

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

                Conceived and designed the experiments: AS PIF GG WJK DE WJFM. Performed the experiments: AS DE. Analyzed the data: AS WJK DE DPF. Contributed reagents/materials/analysis tools: AS WJK DE GG PIF WJFM DPF. Wrote the paper: AS PIF WJK DE DPF.

                Article
                PONE-D-14-13108
                10.1371/journal.pone.0122164
                4372436
                25803607
                9d9f498c-2ad0-4d70-b0b7-9e6ca410f859

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication

                History
                : 25 March 2014
                : 10 February 2015
                Page count
                Figures: 6, Tables: 2, Pages: 28
                Funding
                This project was funded by the Queensland Smithsonian fellowship, Smithsonian Institution National Museum of Natural History, and the University Sunshine Coast Genecology Research Centre. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Custom metadata
                Herbarium voucher specimens and DNA voucher samples are lodged with the Queensland Herbarium BRI. Duplicated DNA vouchers plus extracted DNA is lodged with Smithsonian Institution National Museum of Natural History Kress collections. DNA barcoding data are lodged with the BOLD database www.boldsystems.org. Sequences have been lodged with Genbank www.ncbi.nlm.nih.gov/genbank/. The species lists per subregion are available upon request from the Queensland herbarium https://www.qld.gov.au/environment/plants-animals/plants/herbarium.

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