Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography
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{"title"=>"Sine systemate chaos? A versatile tool for earthworm taxonomy: Non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography", "type"=>"journal", "authors"=>[{"first_name"=>"Rosa", "last_name"=>"Fernández", "scopus_author_id"=>"57193233927"}, {"first_name"=>"Sebastian", "last_name"=>"Kvist", "scopus_author_id"=>"22934705200"}, {"first_name"=>"Jennifer", "last_name"=>"Lenihan", "scopus_author_id"=>"56178037700"}, {"first_name"=>"Gonzalo", "last_name"=>"Giribet", "scopus_author_id"=>"7005356409"}, {"first_name"=>"Alexander", "last_name"=>"Ziegler", "scopus_author_id"=>"9042003300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"373160710", "sgr"=>"84901362826", "pmid"=>"24837238", "scopus"=>"2-s2.0-84901362826", "doi"=>"10.1371/journal.pone.0096617", "issn"=>"19326203"}, "id"=>"4dd1b4ef-2286-3794-86f9-ee7c60d89ab4", "abstract"=>"In spite of the high relevance of lumbricid earthworms ('Oligochaeta': Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (μCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, Aporrectodea caliginosa and A. trapezoides. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that μCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates.", "link"=>"http://www.mendeley.com/research/sine-systemate-chaos-versatile-tool-earthworm-taxonomy-nondestructive-imaging-freshly-fixed-museum-s", "reader_count"=>61, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>12, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Other"=>2, "Student > Master"=>7, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>12, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Other"=>2, "Student > Master"=>7, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Engineering"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>35, "Neuroscience"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Psychology"=>2, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Psychology"=>{"Psychology"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>35}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"New Zealand"=>1, "Hong Kong"=>1, "United States"=>2, "Brazil"=>4, "South Africa"=>1, "United Kingdom"=>1, "Germany"=>1, "Spain"=>2}, "group_count"=>9}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1501178"], "description"=>"<p>(A) Coronal view. (B) Sagittal view. (C) Transverse view. Abbreviations: Buc, buccal cavity; Cco, cerebral commissure; Cgl, calciferous gland; Cip, chaetal insertion point; Cli, clitellum; Cro, crop; Dbv, dorsal blood vessel; Eso, esophagus; Giz, gizzard; Hea, heart; Int, intestine; Mne, metanephridium; Pha, pharynx; Phm, pharyngeal muscle; Pro, prostomium; Sep, septum; Sev, seminal vesicle; Sfu, sperm funnel; Sga, supraesophageal ganglion; Spe, spermatheca; Spp, spermathecal pore; Tes, testes; Typ, typhlosole; Vnc, ventral nerve cord. Roman numerals denote segment numbers.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "2d", "sections", "datasets", "pta-stained", "specimens", "iz", "freshly"], "article_id"=>1029485, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096617.g003", "stats"=>{"downloads"=>2, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_virtual_2D_sections_through_CT_datasets_of_PTA_stained_specimens_of_Aporrectodea_caliginosa_MCZ_IZ_95557_museum_specimen_left_A_trapezoides_MCZ_IZ_24804_freshly_fixed_specimen_center_and_A_trapezoides_MCZ_IZ_95901_museum_specimen_right_/1029485", "title"=>"Selected virtual 2D sections through μCT datasets of PTA-stained specimens of <i>Aporrectodea caliginosa</i> (MCZ IZ 95557, museum specimen, left), <i>A. trapezoides</i> (MCZ IZ 24804, freshly fixed specimen, center), and <i>A. trapezoides</i> (MCZ IZ 95901, museum specimen, right).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-16 02:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1501168"], "description"=>"<p>Anterior facing upwards (A–C) or to the right (D). (A) 2D X-ray projection image of the dataset. (B) Dorsal view of a false-color volume rendering of the dataset. (C) Ventral view. (D) Lateral view. Abbreviations: Cab, chaetae ab; Ccd, chaetae cd; Cli, clitellum; Fpo, female pore; Isf, intersegmental furrow; Mpo, male pore; Per, peristomium; Pro, prostomium; Seg, segment; Spg, sperm groove; Tpu, tubercula pupertatis. Roman numerals denote segment numbers.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "dataset", "pta-stained", "specimen", "iz", "freshly"], "article_id"=>1029475, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096617.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_the_CT_dataset_of_a_PTA_stained_specimen_of_Aporrectodea_caliginosa_MCZ_IZ_24805_freshly_fixed_specimen_/1029475", "title"=>"Visualization of the μCT dataset of a PTA-stained specimen of <i>Aporrectodea caliginosa</i> (MCZ IZ 24805, freshly fixed specimen).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-16 02:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1501182"], "description"=>"<p>(A) The arrow points to a large void inside the digestive tract caused by an air bubble trapped within the gut. (B) The arrows denote streak artifacts caused by highly electron-dense sediment particles located inside the digestive tract. (C) The arrow points to a circular void at the specimen's center caused by insufficient staining of the sample. (D) The arrow points to a ring artifact caused by faulty detector pixels. (E) Insufficient contrast between stained tissue and the surrounding solution due to stain leakage into the surrounding liquid. (F) Blurred image and consequently reduced voxel resolution, caused by specimen movement during scanning, leading to a reduced isotropic voxel resolution.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "encountered", "datasets", "earthworm", "specimens"], "article_id"=>1029489, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096617.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Artifacts_encountered_in_the_956_CT_datasets_of_the_six_earthworm_specimens_analyzed_in_the_course_of_this_study_/1029489", "title"=>"Artifacts encountered in the μCT datasets of the six earthworm specimens analyzed in the course of this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-16 02:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1501190"], "description"=>"<p>Scanning parameters were: source voltage (kV), source current (µA), scanning time (h, min, s), and isotropic voxel resolution of the reconstructed 3D dataset (µm). The embedded hyperlinks provide direct access to the specimen entries in MCZbase (e.g., MCZ IZ 25152).</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "specimens"], "article_id"=>1029497, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096617.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_specimens_used_for_956_CT_scanning_/1029497", "title"=>"List of specimens used for μCT scanning.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-16 02:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1501189"], "description"=>"<p>Specimens shown in dorsal view, with the anterior pointing upwards. (A) Traditional dissection technique based on a longitudinal cut of the dorsal body wall and vertical slitting of individual septa. (B) Traditional dissection technique based on the partial removal of the dorsal body wall, exposing the underlying organs, but leaving the lateral attachments of the septa intact. (C) False-color volume rendering of a μCT dataset (left) and virtual dissection of the same dataset (right) using the ‘wedge dissect’ function in the software Drishti (right). This virtual dissection simulates a longitudinal cut through the body wall and some of the underlying organs. Abbreviations: Cro, crop; Dbv, dorsal blood vessel; Eso, esophagous; Giz, gizzard; Hea, heart; Pha, pharynx; Phm, pharyngeal muscle; Pro, prostomium; Sed, sediment; Sep, septum; Sev, seminal vesicle; Sga, supraesophageal ganglion; Spe, spermatheca.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "dissection", "techniques", "dataset", "earthworm", "iz", "freshly"], "article_id"=>1029496, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096617.g005", "stats"=>{"downloads"=>4, "page_views"=>218, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_traditional_dissection_techniques_with_a_virtual_dissection_based_on_a_CT_dataset_of_the_earthworm_species_Aporrectodea_caliginosa_MCZ_IZ_24805_freshly_fixed_specimen_/1029496", "title"=>"Comparison of traditional dissection techniques with a virtual dissection based on a μCT dataset of the earthworm species <i>Aporrectodea caliginosa</i> (MCZ IZ 24805, freshly fixed specimen).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-16 02:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1501169"], "description"=>"<p>(A) Transverse section at segment X (red), coronal section at the level of the buccal cavity (green), and sagittal section at the level of the typhlosole (blue). (B) Transverse section at segment XXXV (red), coronal section at the level of the spermathecae (green), and sagittal section at the level of the hearts (blue). Abbreviations: Air, trapped air; Buc, buccal cavity; Cli, clitellum; Cro, crop; Dbv, dorsal blood vessel; Dpo, dorsal pore; Eso, esophagus; Giz, gizzard; Hea, heart; Int, intestine; Mne, metanephridium; Pha, pharynx; Phm, pharyngeal muscle; Pro, prostomium; Sep, septum; Sev, seminal vesicle; Sga, supraesophageal ganglion; Sfu, sperm funnel; Spe, spermatheca; Typ, typhlosole; Vbv, Ventral blood vessel; Vnc, ventral nerve cord. Roman numerals denote segment numbers.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "2d", "sections", "dataset", "pta-stained", "specimen", "iz", "freshly"], "article_id"=>1029476, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096617.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_virtual_2D_sections_through_the_CT_dataset_of_a_PTA_stained_specimen_of_Aporrectodea_caliginosa_MCZ_IZ_24805_freshly_fixed_specimen_/1029476", "title"=>"Selected virtual 2D sections through the μCT dataset of a PTA-stained specimen of <i>Aporrectodea caliginosa</i> (MCZ IZ 24805, freshly fixed specimen).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-16 02:45:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1501235", "https://ndownloader.figshare.com/files/1501236", "https://ndownloader.figshare.com/files/1501237", "https://ndownloader.figshare.com/files/1501238"], "description"=>"<div><p>In spite of the high relevance of lumbricid earthworms (‘Oligochaeta’: Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (μCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, <i>Aporrectodea caliginosa</i> and <i>A. trapezoides</i>. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that μCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates.</p></div>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Animal phylogenetics", "Paleontology", "paleobiology", "Paleozoology", "Invertebrate paleontology", "taxonomy", "Animal taxonomy", "Zoology", "Soil science", "Soil ecology", "Diagnostic medicine", "Diagnostic radiology", "tomography", "Computed axial tomography", "systemate", "versatile", "earthworm", "non-destructive", "imaging", "freshly", "specimens", "micro-computed"], "article_id"=>1029537, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Rosa Fernández", "Sebastian Kvist", "Jennifer Lenihan", "Gonzalo Giribet", "Alexander Ziegler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0096617.s001", "https://dx.doi.org/10.1371/journal.pone.0096617.s002", "https://dx.doi.org/10.1371/journal.pone.0096617.s003", "https://dx.doi.org/10.1371/journal.pone.0096617.s004"], "stats"=>{"downloads"=>21, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sine_Systemate_Chaos_A_Versatile_Tool_for_Earthworm_Taxonomy_Non_Destructive_Imaging_of_Freshly_Fixed_and_Museum_Specimens_Using_Micro_Computed_Tomography/1029537", "title"=>"<i>Sine Systemate Chaos?</i> A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-05-16 02:45:43"}

PMC Usage Stats | Further Information

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Relative Metric

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