cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8283641.v1
title: Iba1 & GAD67 8212 GP 1 DCIC panoramas

description: Iba1 & GAD67 8212 GP 1 DCIC panoramas 2019 paper
DOI: 10.6084/m9.figshare.8283695.v1
title: Iba1 & GAD67 8212 GP 1 LCIC panoramas

description: Iba1 & GAD67 8212 GP 1 LCIC panoramas 2019 paper
DOI: 10.6084/m9.figshare.8283593.v1
title: Sapling leaf and root chemistry from 6.6km Jianfengling transect

description: Leaf and root tissue chemsitry for 300 saplings of 50 species (13 faimiles) of tropical trees from Jianfengling, Hainan Island, China. Data were collected during the summer (May to July) of 2017. Laboratory analyses of plant tissue elemental composition of 15 elements (carbon, nitrogen, boron, sodium, magnesium, aluminum, phosphorus, sulfur, potassium, calcium, magnesium, iron, copper, zinc and molybdenum) completed at Florida International and Lousiana State Universities. Soil analyses completed by the Guangzhou Xinhua Agricultural Technical Development Limited Company in Guangzhou, China.
DOI: 10.6084/m9.figshare.8283539
title: CO-ARBitrator Rev2 README

description: 17 June 2019: Revision 2 of the CO-ARBitrator data set is available. It is based on a March 21 2019 snapshot of GenBank, and contains 1,286,434 records of which 249,002 are new since the original revision.<br>The release consists of 4 files: a nucleotide fasta, an incremental nucleotide fasta, an amino acid fasta, and a TSV table. In the TSV table, each row describes a sequence and provides nucleotide and amino acid accession #s and sequences as well as taxonomy.<br><br>The defline format of the fasta files has been changed since the original release, hopefully for the better! In rev 1, deflines contained taxonomy copied verbatim from sequence record pages. These taxonomies are lists of values without rank identifiers; intermediate ranks (e.g. suborder or infraorder) may or may not be present. <br>In rev 2, wherever possible, the taxonomy in the fasta deflines has been retrieved from the NCBI taxonomy browser. Where taxonomy is not available, it is deduced from the "organism" field of the sequence's NSBI record.<br>Example defline:<br> p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #000000; background-color: #ffffff} span.s1 {font-variant-ligatures: no-common-ligatures} &gt;AAG37251|Litoria_nannotis|K_Metazoa__P_Chordata__C_Amphibia__O_Anura__F_Hylidae__G_Litoria__S_nannotis<br>The format is:&gt;Accession|Binomial|TaxonomyTaxonomic ranks are labeled by the first letter of the rank. In the example above, the kingdom (K) is Metazoa, the phylum (P) is Chordata, etc.<br><br>Please address questions, comments, or requests to Phil Heller at philip.heller@sjsu.edu.
DOI: 10.17028/rd.lboro.8283389
title: Supplementary information file for article: 'Integrated change and knowledge management (ICKM) approach for energy retrofits'

description: Supplementary information file for article: 'Integrated change and knowledge management (ICKM) approach for energy retrofits'.<br>ABSTRACT. The importance and benefits of change and dependency management (CDM) and knowledge management (KM) and have been increasingly recognized in the Architecture, Engineering and Construction (AEC) industry. In energy efficiency retrofits, traditional manual methods of managing changes are inefficient and do not fully engage all team members or adequately capture the rationale for changes. In addition, given that knowledge has become a fundamental resource for organizations, it is imperative that any new knowledge generated from change management is captured and disseminated. This paper presents the development of the Integrated Change and Knowledge Management (ICKM) approach based on literature and case studies. The integrated approach established a systematic way to facilitate change and dependency management, capture lessons learned during CDM processes, and support information exchange between different disciplines in change and knowledge management activities. It has been evaluated and refined through two case studies.
DOI: 10.17028/rd.lboro.8283389.v1
title: Supplementary information file for article: 'Integrated change and knowledge management (ICKM) approach for energy retrofits'

description: Supplementary information file for article: 'Integrated change and knowledge management (ICKM) approach for energy retrofits'.<br>ABSTRACT. The importance and benefits of change and dependency management (CDM) and knowledge management (KM) and have been increasingly recognized in the Architecture, Engineering and Construction (AEC) industry. In energy efficiency retrofits, traditional manual methods of managing changes are inefficient and do not fully engage all team members or adequately capture the rationale for changes. In addition, given that knowledge has become a fundamental resource for organizations, it is imperative that any new knowledge generated from change management is captured and disseminated. This paper presents the development of the Integrated Change and Knowledge Management (ICKM) approach based on literature and case studies. The integrated approach established a systematic way to facilitate change and dependency management, capture lessons learned during CDM processes, and support information exchange between different disciplines in change and knowledge management activities. It has been evaluated and refined through two case studies.
DOI: 10.6084/m9.figshare.8283347
title: Haplotype and ribotype diversity of <i>Saxifraga cuneifolia s. l.</i> (Saxifragaceae)

description: <i>Saxifraga cuneifolia</i> L. (sect. <i>Gymnopera</i>, Saxifragaceae) is a plant distributed in the main mountain ranges of southern Europe, from the eastern Pyrenees to the eastern Carpathian. Currently, two subspecies are recognized based on morphological characteristics: <i>S. cuneifolia</i> subsp. <i>cuneifolia</i> grows in the Maritime Alps and North Apennines and <i>S. cuneifolia</i> subsp. <i>robusta</i> is located in the remaining area of distribution. A more delicate form and a smaller number of flowers in <i>S. cuneifolia</i> subsp. <i>cuneifolia</i> are the morphological characteristics that differentiate this subspecies from the widespread <i>S. cuneifolia</i> subsp. <i>robusta</i>. To explore the genetic diversity and the subspecific geographic patterns of <i>S. cuneifolia s. l.</i> we conducted a molecular study of nuclear and plastid sequences. Samples of S<i>. cuneifolia s. l.</i> have been analysed throughout the distribution area of this species. Our results, based on nuclear (ITS) and plastid (<i>rbcL</i>, <i>trnL–F</i>, and <i>psbA–trnH</i>) markers, showed a genetic characterization of both subspecies presenting discriminant haplotypes and ribotypes that confirm the current subspecific systematics.
DOI: 10.6084/m9.figshare.8283347.v1
title: Haplotype and ribotype diversity of <i>Saxifraga cuneifolia s. l.</i> (Saxifragaceae)

description: <i>Saxifraga cuneifolia</i> L. (sect. <i>Gymnopera</i>, Saxifragaceae) is a plant distributed in the main mountain ranges of southern Europe, from the eastern Pyrenees to the eastern Carpathian. Currently, two subspecies are recognized based on morphological characteristics: <i>S. cuneifolia</i> subsp. <i>cuneifolia</i> grows in the Maritime Alps and North Apennines and <i>S. cuneifolia</i> subsp. <i>robusta</i> is located in the remaining area of distribution. A more delicate form and a smaller number of flowers in <i>S. cuneifolia</i> subsp. <i>cuneifolia</i> are the morphological characteristics that differentiate this subspecies from the widespread <i>S. cuneifolia</i> subsp. <i>robusta</i>. To explore the genetic diversity and the subspecific geographic patterns of <i>S. cuneifolia s. l.</i> we conducted a molecular study of nuclear and plastid sequences. Samples of S<i>. cuneifolia s. l.</i> have been analysed throughout the distribution area of this species. Our results, based on nuclear (ITS) and plastid (<i>rbcL</i>, <i>trnL–F</i>, and <i>psbA–trnH</i>) markers, showed a genetic characterization of both subspecies presenting discriminant haplotypes and ribotypes that confirm the current subspecific systematics.
DOI: 10.6084/m9.figshare.8283341
title: Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in <i>Dianella</i> (flax lilies; Asphodelaceae, Hemerocallidoideae)

description: A phylogeny of <i>Dianella</i> is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (<i>trn</i>Q<sup>UUG</sup>–5'<i>rps</i>16, 3'<i>rps</i>16–5'<i>trn</i>K<sup>(UUU)</sup> and <i>rpl</i>14–<i>rps</i>8–<i>inf</i>A–<i>rpl</i>36) and two nuclear markers (ITS and ETS). Accessions included most <i>Dianella</i> species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera <i>Eccremis</i>, <i>Stypandra</i>, <i>Thelionema</i> and <i>Herpolirion.</i> The phylogeny showed <i>Stypandra</i> sister to <i>Herpolirion</i> + <i>Thelionema</i>, and confirmed the monophyly of <i>Dianella.</i> Within <i>Dianella</i>, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by <i>D. serrulata</i> from New Guinea, sister to all other clades of <i>Dianella</i> from Australia and other regions. Tropical North Queensland species, including the <i>D. pavopennacea</i> complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of <i>D. carolinensis</i> (Caroline Islands) and the widespread <i>D. ensifolia</i> from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, <i>D. ensifolia</i> is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the <i>D. revoluta</i> complex. Three New Zealand species (diploid, <i>2n</i> = 16) were found to be related to Norfolk Island <i>D. intermedia</i> (type locality; octoploid, <i>2n</i> = 64). In contrast ‘<i>D. intermedia</i>’ from Lord Howe Island was resolved as sister to the eastern Australian <i>D. caerulea</i> complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ <i>D. longifolia</i> and <i>D. caerulea</i> in Australia, and recognition of more than one species within <i>D. ensifolia</i> and within <i>D. sandwicensis</i> on the Hawaiian Islands.
DOI: 10.6084/m9.figshare.8283281
title: Biological diversity or nomenclatural multiplicity: the Thai freshwater snail <i>Neoradina prasongi</i> Brandt, 1974 (Gastropoda: Thiaridae)

description: A key aspect of evolutionary systematics research is the distinction between nomenclatural multiplicity and biological diversity. Unravelling the latter is only possible by identifying true biological entities, i.e., species and evolutionary lineages instead of an accumulation of nominal taxa. This is particularly difficult to achieve for species with high phenotypic plasticity, such as thiarid freshwater snails, a speciose family notorious for its taxonomic diversity. Exceptionally fraught with problems is a complex of nominal species in the genera <i>Melanoides</i> and <i>Stenomelania.</i> In addition to these genera, morphologically almost indistinguishable shells were the basis for the description of <i>Neoradina prasongi</i> and the establishment of <i>Neoradina.</i> To test whether these shells represent specimens from a distinct evolutionary lineage, we studied representative material of all three genera from Thailand, i.e., <i>Neoradina prasongi</i> and syntopically occurring and/or conchologically similar species, using molecular genetics, shell characters via geometric morphometrics, radula morphology, and reproductive biology. The molecular study of mitochondrial 16S rRNA and COI gene fragments unambiguously supports the distinction of the six species examined, most notably <i>Neoradina prasongi</i> as a distinct lineage. Geometric morphometrics of shell shapes allowed distinguishing species currently assigned to <i>Stenomelania</i> s. str. from the other studied species. Radula characters were uninformative. Our findings confirm the prevalence of different reproductive modes in these viviparous freshwater snails (i.e., the release of larval or juvenile stages). The combined results of our genetic analyses were ambiguous for implications on genus affiliations and did not support the classification of some species as part of <i>Stenomelania</i>, affecting the taxonomic stability of the current conception of these genera. Our results are a crucial first step towards a better understanding of the diversity found within these taxonomically problematic thiarids, emphasizing the need for evolutionary systematics approaches, in order to properly evaluate truly biological diversity in contrast to nomenclatural multiplicity.
DOI: 10.6084/m9.figshare.8283341.v1
title: Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in <i>Dianella</i> (flax lilies; Asphodelaceae, Hemerocallidoideae)

description: A phylogeny of <i>Dianella</i> is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (<i>trn</i>Q<sup>UUG</sup>–5'<i>rps</i>16, 3'<i>rps</i>16–5'<i>trn</i>K<sup>(UUU)</sup> and <i>rpl</i>14–<i>rps</i>8–<i>inf</i>A–<i>rpl</i>36) and two nuclear markers (ITS and ETS). Accessions included most <i>Dianella</i> species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera <i>Eccremis</i>, <i>Stypandra</i>, <i>Thelionema</i> and <i>Herpolirion.</i> The phylogeny showed <i>Stypandra</i> sister to <i>Herpolirion</i> + <i>Thelionema</i>, and confirmed the monophyly of <i>Dianella.</i> Within <i>Dianella</i>, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by <i>D. serrulata</i> from New Guinea, sister to all other clades of <i>Dianella</i> from Australia and other regions. Tropical North Queensland species, including the <i>D. pavopennacea</i> complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of <i>D. carolinensis</i> (Caroline Islands) and the widespread <i>D. ensifolia</i> from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, <i>D. ensifolia</i> is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the <i>D. revoluta</i> complex. Three New Zealand species (diploid, <i>2n</i> = 16) were found to be related to Norfolk Island <i>D. intermedia</i> (type locality; octoploid, <i>2n</i> = 64). In contrast ‘<i>D. intermedia</i>’ from Lord Howe Island was resolved as sister to the eastern Australian <i>D. caerulea</i> complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ <i>D. longifolia</i> and <i>D. caerulea</i> in Australia, and recognition of more than one species within <i>D. ensifolia</i> and within <i>D. sandwicensis</i> on the Hawaiian Islands.
DOI: 10.6084/m9.figshare.8283341.v3
title: Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in <i>Dianella</i> (flax lilies; Asphodelaceae, Hemerocallidoideae)

description: A phylogeny of <i>Dianella</i> is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (<i>trn</i>Q<sup>UUG</sup>–5'<i>rps</i>16, 3'<i>rps</i>16–5'<i>trn</i>K<sup>(UUU)</sup> and <i>rpl</i>14–<i>rps</i>8–<i>inf</i>A–<i>rpl</i>36) and two nuclear markers (ITS and ETS). Accessions included most <i>Dianella</i> species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera <i>Eccremis</i>, <i>Stypandra</i>, <i>Thelionema</i> and <i>Herpolirion.</i> The phylogeny showed <i>Stypandra</i> sister to <i>Herpolirion</i> + <i>Thelionema</i>, and confirmed the monophyly of <i>Dianella.</i> Within <i>Dianella</i>, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by <i>D. serrulata</i> from New Guinea, sister to all other clades of <i>Dianella</i> from Australia and other regions. Tropical North Queensland species, including the <i>D. pavopennacea</i> complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of <i>D. carolinensis</i> (Caroline Islands) and the widespread <i>D. ensifolia</i> from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, <i>D. ensifolia</i> is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the <i>D. revoluta</i> complex. Three New Zealand species (diploid, <i>2n</i> = 16) were found to be related to Norfolk Island <i>D. intermedia</i> (type locality; octoploid, <i>2n</i> = 64). In contrast ‘<i>D. intermedia</i>’ from Lord Howe Island was resolved as sister to the eastern Australian <i>D. caerulea</i> complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ <i>D. longifolia</i> and <i>D. caerulea</i> in Australia, and recognition of more than one species within <i>D. ensifolia</i> and within <i>D. sandwicensis</i> on the Hawaiian Islands.
DOI: 10.6084/m9.figshare.8283341.v2
title: Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in <i>Dianella</i> (flax lilies; Asphodelaceae, Hemerocallidoideae)

description: A phylogeny of <i>Dianella</i> is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (<i>trn</i>Q<sup>UUG</sup>–5'<i>rps</i>16, 3'<i>rps</i>16–5'<i>trn</i>K<sup>(UUU)</sup> and <i>rpl</i>14–<i>rps</i>8–<i>inf</i>A–<i>rpl</i>36) and two nuclear markers (ITS and ETS). Accessions included most <i>Dianella</i> species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera <i>Eccremis</i>, <i>Stypandra</i>, <i>Thelionema</i> and <i>Herpolirion.</i> The phylogeny showed <i>Stypandra</i> sister to <i>Herpolirion</i> + <i>Thelionema</i>, and confirmed the monophyly of <i>Dianella.</i> Within <i>Dianella</i>, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by <i>D. serrulata</i> from New Guinea, sister to all other clades of <i>Dianella</i> from Australia and other regions. Tropical North Queensland species, including the <i>D. pavopennacea</i> complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of <i>D. carolinensis</i> (Caroline Islands) and the widespread <i>D. ensifolia</i> from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, <i>D. ensifolia</i> is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the <i>D. revoluta</i> complex. Three New Zealand species (diploid, <i>2n</i> = 16) were found to be related to Norfolk Island <i>D. intermedia</i> (type locality; octoploid, <i>2n</i> = 64). In contrast ‘<i>D. intermedia</i>’ from Lord Howe Island was resolved as sister to the eastern Australian <i>D. caerulea</i> complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ <i>D. longifolia</i> and <i>D. caerulea</i> in Australia, and recognition of more than one species within <i>D. ensifolia</i> and within <i>D. sandwicensis</i> on the Hawaiian Islands.
DOI: 10.6084/m9.figshare.8283281.v1
title: Biological diversity or nomenclatural multiplicity: the Thai freshwater snail <i>Neoradina prasongi</i> Brandt, 1974 (Gastropoda: Thiaridae)

description: A key aspect of evolutionary systematics research is the distinction between nomenclatural multiplicity and biological diversity. Unravelling the latter is only possible by identifying true biological entities, i.e., species and evolutionary lineages instead of an accumulation of nominal taxa. This is particularly difficult to achieve for species with high phenotypic plasticity, such as thiarid freshwater snails, a speciose family notorious for its taxonomic diversity. Exceptionally fraught with problems is a complex of nominal species in the genera <i>Melanoides</i> and <i>Stenomelania.</i> In addition to these genera, morphologically almost indistinguishable shells were the basis for the description of <i>Neoradina prasongi</i> and the establishment of <i>Neoradina.</i> To test whether these shells represent specimens from a distinct evolutionary lineage, we studied representative material of all three genera from Thailand, i.e., <i>Neoradina prasongi</i> and syntopically occurring and/or conchologically similar species, using molecular genetics, shell characters via geometric morphometrics, radula morphology, and reproductive biology. The molecular study of mitochondrial 16S rRNA and COI gene fragments unambiguously supports the distinction of the six species examined, most notably <i>Neoradina prasongi</i> as a distinct lineage. Geometric morphometrics of shell shapes allowed distinguishing species currently assigned to <i>Stenomelania</i> s. str. from the other studied species. Radula characters were uninformative. Our findings confirm the prevalence of different reproductive modes in these viviparous freshwater snails (i.e., the release of larval or juvenile stages). The combined results of our genetic analyses were ambiguous for implications on genus affiliations and did not support the classification of some species as part of <i>Stenomelania</i>, affecting the taxonomic stability of the current conception of these genera. Our results are a crucial first step towards a better understanding of the diversity found within these taxonomically problematic thiarids, emphasizing the need for evolutionary systematics approaches, in order to properly evaluate truly biological diversity in contrast to nomenclatural multiplicity.