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17 Research products

  • Research data
  • 2012-2021
  • Natural Sciences and Engineering Research Council of Canada
  • CA
  • Transport Research

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Lin, Yaping; Zhan, Aibin; Hernandez, Marco R; Paolucci, Esteban; +2 Authors

    1. Ballast water has been identified as a leading vector for introduction of non-indigenous species (NIS). Recently, the International Maritime Organization (IMO) implemented management standards – D-2 – where all large, commercial ships trading internationally are required to adopt an approved treatment system using technologies such as ultraviolet radiation or chlorination. However, current management regulations are based only on the total abundance of viable taxa transported (i.e., total propagule pressure), largely ignoring species richness (i.e., colonization pressure).2. To determine the efficacy of chlorine treatment in reducing invasion risks and changes in transported biological communities inside ballast tanks, we used DNA metabarcoding-based approaches to estimate colonization pressure (here, the number of species/Operational Taxonomic Units (OTUs) introduced) and relative propagule pressure (relative abundance of each species/OTU) of zooplankton communities in control and chlorine treated tanks during four transatlantic voyages. 3. Our study demonstrated that transport itself did not significantly reduce colonization pressure of zooplankton species, nor did chlorine treatment. Chlorine treatment altered community structure by reducing relative propagule pressure of some taxa such as Mollusca and Rotifera, while increasing relative propagule pressure of some Oligohymenophorea and Copepoda species.4. Synthesis and applications. Chlorine treatment may not reduce invasion risks as much as previously thought. Reduction in total propagule pressure does not mean reduction in abundance of all species equally. While some taxa might experience drastically reduced abundance, others might not change at all or increase due to hatching from dormant stages initiated by chlorine exposure. Therefore, management strategies should consider changes in total propagule pressure and colonization pressure when forecasting risk of new invasions. We therefore recommend adopting new approaches, such as DNA metabarcoding-based methods, to assess the whole biodiversity discharged from ballast water. As species responses to chlorine treatment are variable and affected by concentration, we also recommend a combination of different technologies to reduce introduction risks of aquatic organisms. Supplement to: Lin, Yaping; Zhan, Aibin; Hernandez, Marco R; Paolucci, Esteban; MacIsaac, Hugh J; Briski, Elizabeta (2020): Can chlorination of ballast water reduce biological invasions? Journal of Applied Ecology, 57(2), 331-343 The zip file includes:1. raw_data_clean.fasta: Raw sequence reads of zooplankton in ballast water samples2. raw_data.fasta: OTU representative sequences3. OTU_table.xlsx: OTU table

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    B2FIND
    Dataset . 2019
    Data sources: B2FIND
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    Stoyanovich, Sawyer; Zeyu Yang; Hanson, Mark; Hollebone, Bruce P; +7 Authors

    The main petroleum product transported through pipelines in Canada is diluted bitumen (dilbit), a semi-liquid form of heavy crude oil mixed with natural gas condensates to facilitate transport. The weathering, fate, behaviour, and environmental effects of dilbit are crucial to consider when responding to a spill, however few environmental studies on dilbit have been completed. Here we report on 11-day long experimental spills of dilbit (Cold Lake Winter Blend) in outdoor micro-cosms meant to simulate a low-energy aquatic system containing natural lake water and sedi-ments treated with a low (1:8,000 oil:water) and high (1:800 oil:water) volume of dilbit. In the first 24 hours of the experiment, volatile hydrocarbons quickly evaporated from the dilbit, result-ing in increased dilbit density and viscosity. These changes in dilbit’s physical and chemical properties ultimately led to its submergence after 8 days. We also detected rapid accumulation of polycyclic aromatic compounds in the water column of the treated-microcosms following the spills. Our study provides new information on the environmental fate and behaviour of dilbit in a freshwater environment that will be critical to environmental risk assessments of proposed pipe-line projects. In particular, our study demonstrates the propensity for dilbit to sink under ambient environmental conditions in fresh waters typical of many boreal lakes.

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    Callbeck, Cameron; Lavik, Gaute; Ferdelman, Timothy G; Kuypers, Marcel MM;

    Supplement to: Callbeck, Cameron; Lavik, Gaute; Ferdelman, Timothy G; Fuchs, Bernhard M; Gruber-Vodicka, Harald R; Hach, Philipp F; Littmann, Sten; Schoffelen, Niels J; Kalvelage, Tim; Thomsen, Soeren; Schunck, Harald; Löscher, Carolin R; Schmitz, Ruth A; Kuypers, Marcel MM (2018): Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. The data set includes, sulfide and sulfur concentrations, SUP05 cell densities, as well as denitrification and carbon fixation rates (based on 15N- and 13C-labelled in situ incubation experiments). The transect extends from the sulfidic upper shelf into the sulfide-free offshore oxygen minimum zone.

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    B2FIND
    Dataset . 2017
    Data sources: B2FIND
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    Dickey, James W.E.; Cuthbert, Ross N.; Rea, Michael; Laverty, Ciaran; +10 Authors

    Table S1 The locations of the 20 pet shops surveyed across Northern Ireland :

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    Molis, Markus; Scrosati, Ricardo A; El-Belely, Ehab F; Lesniowski, Thomas; +1 Authors

    1. Environmental stress can influence species traits and performance considerably. Using a seaweed-snail system from NW (Nova Scotia) and NE (Helgoland) Atlantic rocky shores, we examined how physical stress (wave exposure) modulates traits in the seaweed Fucus vesiculosus and indirectly in its main consumer, the periwinkle Littorina obtusata. 2. In both regions, algal tissue toughness increased with wave exposure. Reciprocal-transplant experiments showed that tissue toughness adjusts plastically to the prevailing level of wave exposure. 3. Choice experiments tested the feeding preference of snails from sheltered, exposed, and very exposed habitats for algae from such wave exposures. Snails from exposed and very exposed habitats consumed algal tissues at similar rates irrespective of the exposure of origin of the algae. However, snails from sheltered habitats consumed less algal tissues from very exposed habitats than tissues from sheltered and exposed habitats. Choice assays using reconstituted algal food (triturated during preparation) identified high thallus toughness as the explanation for the low preference of snails from sheltered habitats for algae from very exposed habitats. 4. Ultrastructural analyses of radulae indicated that rachidian teeth were longest and the number of cusps in lateral teeth (grazing-relevant traits) was highest in snails from very exposed habitats, suggesting that radulae are best suited to rupture tough algal tissues in such snails. 5. No-choice feeding experiments revealed that these radular traits are also phenotypically plastic, as they adjust to the toughness of the algal food. 6. Synthesis. This study indicates that the observed plasticity in the feeding ability of snails is mediated by wave exposure through phenotypic plasticity in the tissue toughness of algae. Thus, plasticity in consumers and their resource species may reduce the potential effects of physical stress on their interaction. Measurements on the rocky shores in Tor Bay, Nova Scotia, Canada (between 45.10644-45.11153 N and 61.21160-61.21700 W) and Helgoland (Helgoland (Bunker: 54.18806 N, 7.87436 E; Augusta Mole: 54.18931 N 7.89972 E; Nord-Ost Hafen, 54.18311 N, 7.88947 E, and Südhafen, 54.17819 N, 7.89417 E) to quantify1. maximum water velocity2. puncture force of Fucus vesiculosus thalli from sites of different wave exposure3. Littorina obtusata consumption of Fucus vesiculosus (fresh (both shores) and reconsituted (only Nova Scotia) from sites of different wave exposure 4. morphological traits (central teeth cusp length, number of cusps on lateral teeth) of field collected Littorina obtusata radula from different sites of wave exposure (only Nova Scotia) 5. morphological traits (central teeth cusp length, number of cusps on lateral teeth) of the Littorina obtusata radula from different sites of wave exposure feed with Fucus vesiculosus from different sites of wave exposre (only Nova Scotia) Supplement to: Molis, Markus; Scrosati, Ricardo A; El-Belely, Ehab F; Lesniowski, Thomas; Wahl, Martin (2015): Wave-induced changes in seaweed toughness entail plastic modifications in snail traits maintaining consumption efficacy. Journal of Ecology, 103(4), 851-859

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    B2FIND
    Dataset . 2015
    Data sources: B2FIND
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    Briski, Elizabeta; Ghabooli, Sara; Bailey, Sarah A; MacIsaac, Hugh J;

    Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61% of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78% for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63% respectively, while those for terrestrial NIS increased to 74 and 88% respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data - mostly aquatic ones - encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time. Supplement to: Briski, Elizabeta; Ghabooli, Sara; Bailey, Sarah A; MacIsaac, Hugh J (2016): Are genetic databases sufficiently populated to detect non-indigenous species? Biological Invasions, 18(7), 1911-1922

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    B2FIND
    Dataset . 2016
    Data sources: B2FIND
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    Baxter, Alan T; Hannington, Mark D; Stewart, Margaret S; Emberley, Justin M; +7 Authors

    We compared Centroid Moment Tensors (CMTs), calculated for large (Mw >5), shallow (<30 km) seismic events to the orientations of seafloor lineaments (n = 4000) mapped throughout the Lau Basin, in the SW Pacific. Ship-based multibeam was combined with vertical gravity gradient data to provide comprehensive coverage to create the lineament map. By comparing the possible focal planes of the CMTs to the orientations of the lineaments, the most likely fault plane solutions were selected, thus classifying the faults and establishing the nature of the highly variable stress regimes in the basin. We resolved the strike, dip and dip direction of 308 faults, and classified 258 additional structures by fault type. The majority of the table was data downloaded from the Global Centroid Moment Tensor (GCMT) database (www.globalcmt.org: accessed October 2018). For more details about the column headers consult the GCMT database website. New data from this study include the latitude and longitude error estimates (in meters), the classified faults (column: 'fault_type'), and the stress domain (column: 'stress_domain'), allocated to each of the classified faults.

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    B2FIND
    Dataset . 2020
    Data sources: B2FIND
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    Sunjoo Joo; Wang, Ming; Lui, Gary; Lee, Jenny; +5 Authors

    Table S1. Genomic resources used in this study. Table S2. Archaeplastidal homeobox collection of TALE protein analyzed in this study. Table S3. KNOX domain homology among KNOX classes. Table S4. Primers used in this study. Table S5. Yeast-two-hybrid constructs used in this study. Table S6. Homeobox profile in Trebouxiophyceae. (XLSX 370 kb)

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    Dickey, James W.E.; Cuthbert, Ross N.; Rea, Michael; Laverty, Ciaran; +10 Authors

    R Script Biplot Creation :

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    Dickey, James W.E.; Cuthbert, Ross N.; Rea, Michael; Laverty, Ciaran; +10 Authors

    R Script Triplot Creation :

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17 Research products
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    Lin, Yaping; Zhan, Aibin; Hernandez, Marco R; Paolucci, Esteban; +2 Authors

    1. Ballast water has been identified as a leading vector for introduction of non-indigenous species (NIS). Recently, the International Maritime Organization (IMO) implemented management standards – D-2 – where all large, commercial ships trading internationally are required to adopt an approved treatment system using technologies such as ultraviolet radiation or chlorination. However, current management regulations are based only on the total abundance of viable taxa transported (i.e., total propagule pressure), largely ignoring species richness (i.e., colonization pressure).2. To determine the efficacy of chlorine treatment in reducing invasion risks and changes in transported biological communities inside ballast tanks, we used DNA metabarcoding-based approaches to estimate colonization pressure (here, the number of species/Operational Taxonomic Units (OTUs) introduced) and relative propagule pressure (relative abundance of each species/OTU) of zooplankton communities in control and chlorine treated tanks during four transatlantic voyages. 3. Our study demonstrated that transport itself did not significantly reduce colonization pressure of zooplankton species, nor did chlorine treatment. Chlorine treatment altered community structure by reducing relative propagule pressure of some taxa such as Mollusca and Rotifera, while increasing relative propagule pressure of some Oligohymenophorea and Copepoda species.4. Synthesis and applications. Chlorine treatment may not reduce invasion risks as much as previously thought. Reduction in total propagule pressure does not mean reduction in abundance of all species equally. While some taxa might experience drastically reduced abundance, others might not change at all or increase due to hatching from dormant stages initiated by chlorine exposure. Therefore, management strategies should consider changes in total propagule pressure and colonization pressure when forecasting risk of new invasions. We therefore recommend adopting new approaches, such as DNA metabarcoding-based methods, to assess the whole biodiversity discharged from ballast water. As species responses to chlorine treatment are variable and affected by concentration, we also recommend a combination of different technologies to reduce introduction risks of aquatic organisms. Supplement to: Lin, Yaping; Zhan, Aibin; Hernandez, Marco R; Paolucci, Esteban; MacIsaac, Hugh J; Briski, Elizabeta (2020): Can chlorination of ballast water reduce biological invasions? Journal of Applied Ecology, 57(2), 331-343 The zip file includes:1. raw_data_clean.fasta: Raw sequence reads of zooplankton in ballast water samples2. raw_data.fasta: OTU representative sequences3. OTU_table.xlsx: OTU table

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    B2FIND
    Dataset . 2019
    Data sources: B2FIND
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    Stoyanovich, Sawyer; Zeyu Yang; Hanson, Mark; Hollebone, Bruce P; +7 Authors

    The main petroleum product transported through pipelines in Canada is diluted bitumen (dilbit), a semi-liquid form of heavy crude oil mixed with natural gas condensates to facilitate transport. The weathering, fate, behaviour, and environmental effects of dilbit are crucial to consider when responding to a spill, however few environmental studies on dilbit have been completed. Here we report on 11-day long experimental spills of dilbit (Cold Lake Winter Blend) in outdoor micro-cosms meant to simulate a low-energy aquatic system containing natural lake water and sedi-ments treated with a low (1:8,000 oil:water) and high (1:800 oil:water) volume of dilbit. In the first 24 hours of the experiment, volatile hydrocarbons quickly evaporated from the dilbit, result-ing in increased dilbit density and viscosity. These changes in dilbit’s physical and chemical properties ultimately led to its submergence after 8 days. We also detected rapid accumulation of polycyclic aromatic compounds in the water column of the treated-microcosms following the spills. Our study provides new information on the environmental fate and behaviour of dilbit in a freshwater environment that will be critical to environmental risk assessments of proposed pipe-line projects. In particular, our study demonstrates the propensity for dilbit to sink under ambient environmental conditions in fresh waters typical of many boreal lakes.

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    Callbeck, Cameron; Lavik, Gaute; Ferdelman, Timothy G; Kuypers, Marcel MM;

    Supplement to: Callbeck, Cameron; Lavik, Gaute; Ferdelman, Timothy G; Fuchs, Bernhard M; Gruber-Vodicka, Harald R; Hach, Philipp F; Littmann, Sten; Schoffelen, Niels J; Kalvelage, Tim; Thomsen, Soeren; Schunck, Harald; Löscher, Carolin R; Schmitz, Ruth A; Kuypers, Marcel MM (2018): Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. The data set includes, sulfide and sulfur concentrations, SUP05 cell densities, as well as denitrification and carbon fixation rates (based on 15N- and 13C-labelled in situ incubation experiments). The transect extends from the sulfidic upper shelf into the sulfide-free offshore oxygen minimum zone.

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    B2FIND
    Dataset . 2017
    Data sources: B2FIND
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    Dickey, James W.E.; Cuthbert, Ross N.; Rea, Michael; Laverty, Ciaran; +10 Authors

    Table S1 The locations of the 20 pet shops surveyed across Northern Ireland :

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    Molis, Markus; Scrosati, Ricardo A; El-Belely, Ehab F; Lesniowski, Thomas; +1 Authors

    1. Environmental stress can influence species traits and performance considerably. Using a seaweed-snail system from NW (Nova Scotia) and NE (Helgoland) Atlantic rocky shores, we examined how physical stress (wave exposure) modulates traits in the seaweed Fucus vesiculosus and indirectly in its main consumer, the periwinkle Littorina obtusata. 2. In both regions, algal tissue toughness increased with wave exposure. Reciprocal-transplant experiments showed that tissue toughness adjusts plastically to the prevailing level of wave exposure. 3. Choice experiments tested the feeding preference of snails from sheltered, exposed, and very exposed habitats for algae from such wave exposures. Snails from exposed and very exposed habitats consumed algal tissues at similar rates irrespective of the exposure of origin of the algae. However, snails from sheltered habitats consumed less algal tissues from very exposed habitats than tissues from sheltered and exposed habitats. Choice assays using reconstituted algal food (triturated during preparation) identified high thallus toughness as the explanation for the low preference of snails from sheltered habitats for algae from very exposed habitats. 4. Ultrastructural analyses of radulae indicated that rachidian teeth were longest and the number of cusps in lateral teeth (grazing-relevant traits) was highest in snails from very exposed habitats, suggesting that radulae are best suited to rupture tough algal tissues in such snails. 5. No-choice feeding experiments revealed that these radular traits are also phenotypically plastic, as they adjust to the toughness of the algal food. 6. Synthesis. This study indicates that the observed plasticity in the feeding ability of snails is mediated by wave exposure through phenotypic plasticity in the tissue toughness of algae. Thus, plasticity in consumers and their resource species may reduce the potential effects of physical stress on their interaction. Measurements on the rocky shores in Tor Bay, Nova Scotia, Canada (between 45.10644-45.11153 N and 61.21160-61.21700 W) and Helgoland (Helgoland (Bunker: 54.18806 N, 7.87436 E; Augusta Mole: 54.18931 N 7.89972 E; Nord-Ost Hafen, 54.18311 N, 7.88947 E, and Südhafen, 54.17819 N, 7.89417 E) to quantify1. maximum water velocity2. puncture force of Fucus vesiculosus thalli from sites of different wave exposure3. Littorina obtusata consumption of Fucus vesiculosus (fresh (both shores) and reconsituted (only Nova Scotia) from sites of different wave exposure 4. morphological traits (central teeth cusp length, number of cusps on lateral teeth) of field collected Littorina obtusata radula from different sites of wave exposure (only Nova Scotia) 5. morphological traits (central teeth cusp length, number of cusps on lateral teeth) of the Littorina obtusata radula from different sites of wave exposure feed with Fucus vesiculosus from different sites of wave exposre (only Nova Scotia) Supplement to: Molis, Markus; Scrosati, Ricardo A; El-Belely, Ehab F; Lesniowski, Thomas; Wahl, Martin (2015): Wave-induced changes in seaweed toughness entail plastic modifications in snail traits maintaining consumption efficacy. Journal of Ecology, 103(4), 851-859

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    B2FIND
    Dataset . 2015
    Data sources: B2FIND
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    Briski, Elizabeta; Ghabooli, Sara; Bailey, Sarah A; MacIsaac, Hugh J;

    Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61% of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78% for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63% respectively, while those for terrestrial NIS increased to 74 and 88% respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data - mostly aquatic ones - encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time. Supplement to: Briski, Elizabeta; Ghabooli, Sara; Bailey, Sarah A; MacIsaac, Hugh J (2016): Are genetic databases sufficiently populated to detect non-indigenous species? Biological Invasions, 18(7), 1911-1922

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    B2FIND
    Dataset . 2016
    Data sources: B2FIND
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    Baxter, Alan T; Hannington, Mark D; Stewart, Margaret S; Emberley, Justin M; +7 Authors

    We compared Centroid Moment Tensors (CMTs), calculated for large (Mw >5), shallow (<30 km) seismic events to the orientations of seafloor lineaments (n = 4000) mapped throughout the Lau Basin, in the SW Pacific. Ship-based multibeam was combined with vertical gravity gradient data to provide comprehensive coverage to create the lineament map. By comparing the possible focal planes of the CMTs to the orientations of the lineaments, the most likely fault plane solutions were selected, thus classifying the faults and establishing the nature of the highly variable stress regimes in the basin. We resolved the strike, dip and dip direction of 308 faults, and classified 258 additional structures by fault type. The majority of the table was data downloaded from the Global Centroid Moment Tensor (GCMT) database (www.globalcmt.org: accessed October 2018). For more details about the column headers consult the GCMT database website. New data from this study include the latitude and longitude error estimates (in meters), the classified faults (column: 'fault_type'), and the stress domain (column: 'stress_domain'), allocated to each of the classified faults.

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    B2FIND
    Dataset . 2020
    Data sources: B2FIND
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    Sunjoo Joo; Wang, Ming; Lui, Gary; Lee, Jenny; +5 Authors

    Table S1. Genomic resources used in this study. Table S2. Archaeplastidal homeobox collection of TALE protein analyzed in this study. Table S3. KNOX domain homology among KNOX classes. Table S4. Primers used in this study. Table S5. Yeast-two-hybrid constructs used in this study. Table S6. Homeobox profile in Trebouxiophyceae. (XLSX 370 kb)

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    Dickey, James W.E.; Cuthbert, Ross N.; Rea, Michael; Laverty, Ciaran; +10 Authors

    R Script Biplot Creation :

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    Dickey, James W.E.; Cuthbert, Ross N.; Rea, Michael; Laverty, Ciaran; +10 Authors

    R Script Triplot Creation :

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