Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography

Fernández, Rosa; Kvist, Sebastian; Lenihan, Jennifer; Giribet, Gonzalo; Ziegler, Alexander

doi:10.1371/journal.pone.0096617

Cited by 58 publications

(68 citation statements)

References 61 publications

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“…Some of these taxonomic difficulties may be alleviated by recent developments in imagery for the description of internal morphology using Micro-Computed Tomography (Fernández et al 2014), but lack of taxonomic expertise remains limiting. In recent years, the introduction of DNA barcoding has effectively aided species discrimination, identification of new taxa, reconstruction of phylogeny, and biodiversity assessments in numerous invertebrate groups, including earthworms (King et al 2008;Chang & James 2011;Decaëns et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Molecular identification and distribution of native and exotic earthworms in New Zealand human-modified soils

Kim¹,

Dickinson²,

Bowie³

et al. 2017

NZ J Ecol

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Important knowledge gaps remain with regards to the ecology and the systematics of New Zealand's native earthworms. With many putative new species yet to be described, often specimens cannot be named, which makes species inventory, monitoring and community comparisons difficult. Our work aimed to identify new putative taxa of New Zealand native species of earthworms, and describe their distribution in selected human-modified ecosystems. A total of 24 earthworm taxa (13 native and 11 exotic) were identified using a DNA barcoding approach focusing on 16S rDNA and COI (cytochrome oxidase subunit 1). The combination of morphological and molecular analyses were complementary in elucidating species identity. However, of the 13 native taxa, eight could not be named and are likely to be undescribed species from the genera Octochaetus, Maoridrilus and Deinodrilus. Most native species appeared to have a restricted geographic distribution linked to soil conditions, in particular pH and organic matter.

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Section: Introductionmentioning

confidence: 99%

Molecular identification and distribution of native and exotic earthworms in New Zealand human-modified soils

Kim¹,

Dickinson²,

Bowie³

et al. 2017

NZ J Ecol

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“…The difference between X‐ray CT and μ‐CT is merely the level of detail: μ‐CT works at the micrometer range (Medical Subject Headings—MeSH) and has become an invaluable tool in the study of several organs and organ systems in arthropods (see a review in Westneat et al., 2008; Metscher, 2013; Sombke et al., 2015) and other invertebrates (Carbayo & Lenihan, 2016; Fernández et al., 2014). This technique allows spatial resolution in the 1–10 μm range (i.e., spanning the range from whole cells down to the level of single organelles) and a temporal resolution of less than 100 ms.…”

Section: X‐ray‐based Computed Tomography (X‐ray Ct and μ‐Ct)mentioning

confidence: 99%

“…To date, these techniques have been more commonly used for taxonomy, phylogeny, and physiology (Beutel, Friedrich, Ge, & Yang, 2014; Fernández et al., 2014; Friedrich & Beutel, 2008; Metscher, 2013). …”

Section: Application Of X‐ray Computed Tomography In Ecological Studiesmentioning

confidence: 99%

“…Fields such as taxonomy (Akkari, Enghoff, & Metscher, 2015; Faulwetter, Vasileiadou, Kouratoras, Dailianis, & Arvanitidis, 2013; Fernández, Kvist, Lenihan, Giribet, & Ziegler, 2014) and morphology (Mattei, Riccio, Avila, & Wolfner, 2015; Wipfler et al., 2016) have greatly benefited from μ‐CT technique. However, most studies to date have focused on in‐depth studies of single individuals, and organisms′ responses to environmental drivers were only rarely considered.…”

Section: Introductionmentioning

confidence: 99%

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X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Gutiérrez

Ott

Töpperwien

et al. 2018

Ecology and Evolution

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Imaging techniques are a cornerstone of contemporary biology. Over the last decades, advances in microscale imaging techniques have allowed fascinating new insights into cell and tissue morphology and internal anatomy of organisms across kingdoms. However, most studies so far provided snapshots of given reference taxa, describing organs and tissues under “idealized” conditions. Surprisingly, there is an almost complete lack of studies investigating how an organism′s internal morphology changes in response to environmental drivers. Consequently, ecology as a scientific discipline has so far almost neglected the possibilities arising from modern microscale imaging techniques. Here, we provide an overview of recent developments of X‐ray computed tomography as an affordable, simple method of high spatial resolution, allowing insights into three‐dimensional anatomy both in vivo and ex vivo. We review ecological studies using this technique to investigate the three‐dimensional internal structure of organisms. In addition, we provide practical comparisons between different preparation techniques for maximum contrast and tissue differentiation. In particular, we consider the novel modality of phase contrast by self‐interference of the X‐ray wave behind an object (i.e., phase contrast by free space propagation). Using the cricket Acheta domesticus (L.) as model organism, we found that the combination of FAE fixative and iodine staining provided the best results across different tissues. The drying technique also affected contrast and prevented artifacts in specific cases. Overall, we found that for the interests of ecological studies, X‐ray computed tomography is useful when the tissue or structure of interest has sufficient contrast that allows for an automatic or semiautomatic segmentation. In particular, we show that reconstruction schemes which exploit phase contrast can yield enhanced image quality. Combined with suitable specimen preparation and automated analysis, X‐ray CT can therefore become a promising quantitative 3D imaging technique to study organisms′ responses to environmental drivers, in both ecology and evolution.

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“…Utility of microcomputed CT scanning for the taxonomy of Actiniaria: In this study we evaluate the utility of micro-CT imaging for the taxonomy and systematics of sea anemones, which has been possible only as a result of recent protocol modifications of contrast enhancement in soft-bodied invertebrates (e.g., Metscher, 2009aMetscher, , 2009bFaulwetter et al, 2013aFaulwetter et al, , 2013bDescamps et al, 2014;Paterson et al, 2014;Fernández et al, 2014;Tessler et al, 2016;Holst et al, 2016). The appeal of micro-CT scanning for sea anemone studies is its potential to facilitate and improve characterization of morphological characters used in the taxonomy of the group especially in regard to the tridimensional anatomical representations based on of micro-CT images.…”

Section: Fig 12 (Continued) Diadumene Lineatamentioning

confidence: 99%

Sea Anemones through X-Rays: Visualization of Two Species ofDiadumene(Cnidaria, Actiniaria) Using Micro-CT

Gusmão

Grajales

Rodríguez

2018

American Museum Novitates

821

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Diadumenidae is a monogeneric family comprised of 10 valid species in the genus Diadumene. Although these species are distributed in all but the Southern Ocean, Diadumene lineata is a cosmopolitan species and one of the most widely distributed marine organisms. Recent phylogenetic analyses with multiple species have recovered Diadumenidae as a monophyletic group with high support. Although generic placement is straightforward, species-level identifications within Diadumene are difficult because species are defined by a mosaic of characters that vary in degree rather than kind. Two species of the genus have been recorded in the southwestern Atlantic: D. paranaensis along the south coast of Brazil and D. lineata along the southeast and northeast coasts of Brazil as well as in Argentina. Here we record D. leucolena for the first time in the southern hemisphere and describe D. manezinha, sp. nov., raising to four the number of species of Diadumene for Brazil and to 11 worldwide. We incorporated microcomputed tomography (micro-CT) into the description of both species in the first application of the method for Actiniaria. We evaluate the utility of micro-CT imaging and its potential to generate fast, low-cost, and high-resolution datasets despite the anemone's low-density soft tissue. We present a protocol for sample handling, chemical staining, and scanning parameters that resulted in satisfactory imaging of the two specimens examined. We also analyze advantages and limitations of using micro-CT over traditional techniques in the study of sea anemones.

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Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography

Cited by 58 publications

References 61 publications

Molecular identification and distribution of native and exotic earthworms in New Zealand human-modified soils

Molecular identification and distribution of native and exotic earthworms in New Zealand human-modified soils

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Sea Anemones through X-Rays: Visualization of Two Species ofDiadumene(Cnidaria, Actiniaria) Using Micro-CT

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