Dataset Information

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

ABSTRACT: To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

SUBMITTER: Pei N

PROVIDER: S-EPMC4601009 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

Pei Nancai N Erickson David L DL Chen Bufeng B Ge Xuejun X Mi Xiangcheng X Swenson Nathan G NG Zhang Jin-Long JL Jones Frank A FA Huang Chun-Lin CL Ye Wanhui W Hao Zhanqing Z Hsieh Chang-Fu CF Lum Shawn S Bourg Norman A NA Parker John D JD Zimmerman Jess K JK McShea William J WJ Lopez Ida C IC Sun I-Fang IF Davies Stuart J SJ Ma Keping K Kress W John WJ

Scientific reports 20151012

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes ...[more]

PMID: 26456472

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Project description:BackgroundChronic obstructive pulmonary disease (COPD) is a progressive chronic condition. Improvements in therapies have resulted in better patient outcomes. The use of technology such as telemonitoring as an additional intervention is aimed at enhancing care and reducing unnecessary acute hospital service use. The influence of verbal communication between health staff and patients to inform decision making regarding use of acute hospital services within telemonitoring studies has not been assessed.MethodA systematic overview of published systematic reviews of COPD and telemonitoring was conducted using an a priori protocol to ascertain the impact of verbal communication in telemonitoring studies on health service outcomes such as emergency department attendances, hospitalisation and hospital length of stay. The search of the following electronic databases: Cochrane Library, Medline, Pubmed, CINAHL, Embase, TROVE, Australian Digital Thesis and Proquest International Dissertations and Theses was conducted in 2017 and updated in September 2019.ResultsSix systematic reviews were identified. All reviews involved home monitoring of COPD symptoms and biometric data. Included reviews reported 5-28 studies with sample sizes ranging from 310 to 2891 participants. Many studies reported in the systematic reviews were excluded as they were telephone support, cost effectiveness studies, and/or did not report the outcomes of interest for this overview. Irrespective of group assignment, verbal communication with the health or research team did not alter the emergency attendance or hospitalisation outcome. The length of stay was longer for those who were assigned home telemonitoring in the majority of studies.ConclusionThis overview of telemonitoring for COPD had small sample sizes and a wide variety of included studies. Communication was not consistent in all included studies. Understanding the context of communication with study participants and the decision-making process for referring patients to various health services needs to be reported in future studies of telemonitoring and COPD.

Project description:Taxa in the genus Melanelia (Parmeliaceae, Ascomycota) belong to a group of saxicolous lichens with brown to black foliose thalli, which have recently undergone extensive changes in circumscription. Taxa belonging to Parmeliaceae are prolific producers of bioactive compounds, which have also been traditionally used for chemotaxonomic purposes. However, the chemical diversity of the genus Melanelia and the use of chemical data for species discrimination in this genus are largely unexplored. In addition, identification based on morphological characters is challenging due to few taxonomically informative characters. Molecular identification methods, such as DNA barcoding, have rarely been applied to this genus. This study aimed to identify the Melanelia species from Iceland using DNA barcoding approach, and to explore their chemical diversity using chemical profiling. Chemometric tools were used to see if lichen metabolite profiles determined by LC-MS could be used for the identification of Icelandic Melanelia species. Barcoding using the fungal nuclear ribosomal internal transcribed spacer region (nrITS) successfully identified three Melalenlia species occurring in Iceland, together with Montanelia disjuncta (Basionym: Melanelia disjuncta). All species formed monophyletic clades in the neighbor-joining nrITS gene tree. However, high intraspecific genetic distance of M. stygia suggests the potential of unrecognized species lineages. Principal component analysis (PCA) of metabolite data gave a holistic overview showing that M. hepatizon and M. disjuncta were distinct from the rest, without the power to separate M. agnata and M. stygia due to their chemical similarity. Orthogonal partial least-squares to latent structures-discriminate analysis (OPLS-DA), however, successfully distinguished M. agnata and M. stygia by identifying statistically significant metabolites, which lead to class differentiation. This work has demonstrated the potential of DNA barcoding, chemical profiling and chemometrics in identification of Melanelia species.

Dataset Information

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

Publications

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

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