Eupolybothrus cavernicolus Komerički &amp;amp; Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data

Stoev, Pavel; Komerički, Ana; Akkari, Nesrine; Liu, Shanlin; Zhou, Xin; Weigand, Alexander; Hostens, Jeroen; Hunter, Chris; Edmunds, Scott; Porco, David; Zapparoli, Marzio; Georgiev, Teodor; Mietchen, Daniel; Roberts, David; Faulwetter, Sarah; Smith, Vincent; Penev, Lyubomir

doi:10.3897/bdj.1.e1013

Cited by 51 publications

(65 citation statements)

References 43 publications

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“…Analyses that use the number of authors per species description as a proxy for effort [19] ignore the global trend for an increasing number of authors per paper [2], and assume that the effort required per species description has remained constant over time. An alternative interpretation is that the quality of taxonomic description is increasing over time [36], reflecting both increased thoroughness and the availability of new technologies [37,5]. Rather than try and estimate an unknown (the number of species remaining to be described), here I focus on the current state of taxonomic knowledge.…”

Section: Taxonomymentioning

confidence: 99%

DNA barcoding and taxonomy: dark taxa and dark texts

Page

2016

Preprint

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Both classical taxonomy and DNA barcoding are engaged in the task of digitising the living world. Much of the taxonomic literature remains undigitised. The rise of open access publishing this century, and the freeing of older literature from the shackles of copyright has greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid-to late twentieth century remains offline ("dark texts"). DNA barcoding is generating a wealth of computable data that in many ways is much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These "dark taxa" hamper the classical method of integrating biodiversity data using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature, and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global "digital dashboard" to assess the extent to which biodiversity data is available online.

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Section: Taxonomymentioning

confidence: 99%

DNA barcoding and taxonomy: dark taxa and dark texts

Page

2016

Preprint

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“…Concerned with growing disappearance rates, some scientists have encouraged moving to a so-called 'turbo taxonomy' approach, where rapid species description is needed to manage conservation [68]. A demonstrative collaboration between GigaScience and Pensoft Publishers has pushed the boundaries of opening up by the digital era further still, presenting an innovative approach to describing new species by creating a new kind of 'specimen', the 'cybertype' [78]. This consists of detailed and three-dimensional (3D) computer images of a specimen that can be downloaded anywhere in the world and a swathe of data types to suit modern biology, including its gene catalogue (transcriptome), DNA barcodes, and video of the live animal, in addition to the traditional morphological description.…”

Section: Tools For Taxonomy 20: Sea Urchins Earthwormsmentioning

confidence: 99%

Experiences in integrated data and research object publishing using GigaDB

Edmunds

Hunter

et al. 2016

Int J Digit Libr

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In the era of computation and data-driven research, traditional methods of disseminating research are no longer fit-for-purpose. New approaches for disseminating data, methods and results are required to maximize knowledge discovery. The "long tail" of small, unstructured datasets is well catered for by a number of general-purpose repositories, but there has been less support for "big data". Outlined here are our experiences in attempting to tackle the gaps in publishing large-scale, computationally intensive research.GigaScience is an open-access, open-data journal aiming to revolutionize large-scale biological data dissemination, organization and re-use. Through use of the data handling infrastructure of the genomics centre BGI, GigaScience links standard manuscript publication with an integrated database (GigaDB) that hosts all associated data, and provides additional data analysis tools and computing resources. Furthermore, the supporting workflows and methods are also integrated to make published articles more transparent and open. GigaDB has released many new and previously unpublished datasets and data types, including as urgently needed data to tackle infectious disease outbreaks, cancer and the growing food crisis. Other "executable" research objects, such as workflows, virtual machines and software from several GigaScience articles have been archived and shared in reproducible, transparent and usable formats. With data citation producing evidence Office for National Statistics, Duffryn, Government Buildings, Cardiff Rd, Newport NP10 8XG, UK of, and credit for, its use in the wider research community, GigaScience demonstrates a move towards more executable publications. Here data analyses can be reproduced and built upon by users without coding backgrounds or heavy computational infrastructure in a more democratized manner.

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“…In the last years, this situation is changing and micro-CT has become a powerful tool to visually enhance and support diagnostic species delimitations, from single species descriptions to revisions. While initially used for polychaetes (Faulwetter et al 2013), myriapods (Stoev et al 2013, Akkari et al 2015), spiders (Michalik and Ramírez 2013), earthworms (Fernández et al 2014), and flatworms (Carbayo and Lenihan 2016, Carbayo et al 2016), micro-CT has evolved into a cutting-edge tool increasingly applied for ant taxonomy (Csősz 2012, Fischer et al 2016, Sarnat et al 2016, Agavekar et al 2017, Hita Garcia et al 2017a, 2017b). A detailed and critical assessment of the technology and its applications for ant taxonomy was provided by Hita Garcia et al (2017b).…”

Section: Introductionmentioning

confidence: 99%

Systematics of the ant genus Proceratium Roger (Hymenoptera, Formicidae, Proceratiinae) in China – with descriptions of three new species based on micro-CT enhanced next-generation-morphology

Staab

Garcia²,

Liu³

et al. 2018

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The genus Proceratium Roger, 1863 contains cryptic, subterranean ants that are seldom sampled and rare in natural history collections. Furthermore, most Proceratium specimens are extremely hairy and, due to their enlarged and curved gaster, often mounted suboptimally. As a consequence, the poorly observable physical characteristics of the material and its scarcity result in a rather challenging alpha taxonomy of this group. In this study, the taxonomy of the Chinese Proceratium fauna is reviewed and updated by combining examinations of traditional light microscopy with x-ray microtomography (micro-CT). Based on micro-CT scans of seven out of eight species, virtual 3D surface models were generated that permit in-depth comparative analyses of specimen morphology in order to overcome the difficulties to examine physical material of Proceratium. Eight Chinese species are recognized, of which three are newly described: Proceratium bruelheidei Staab, Xu & Hita Garcia, sp. n. and P. kepingmai sp. n. belong to the P. itoi clade and have been collected in the subtropical forests of southeast China, whereas P. shohei sp. n. belongs to the P. stictum clade and it is only known from a tropical forest of Yunnan Province. Proceratium nujiangense Xu, 2006 syn. n. is proposed as a junior synonym of P. zhaoi Xu, 2000. These taxonomic acts raise the number of known Chinese Proceratium species to eight. In order to integrate the new species into the existing taxonomic system and to facilitate identifications, an illustrated key to the worker caste of all Chinese species is provided, supplemented by species accounts with high-resolution montage images and still images of volume renderings of 3D models based on micro-CT. Moreover, cybertype datasets are provided for the new species, as well as digital datasets for the remaining species that include the raw micro-CT scan data, 3D surface models, 3D rotation videos, and all light photography and micro-CT still images. These datasets are available online (Dryad, Staab et al. 2018, http://dx.doi.org/10.5061/dryad.h6j0g4p).

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Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data

Cited by 51 publications

References 43 publications

DNA barcoding and taxonomy: dark taxa and dark texts

DNA barcoding and taxonomy: dark taxa and dark texts

Experiences in integrated data and research object publishing using GigaDB

Systematics of the ant genus Proceratium Roger (Hymenoptera, Formicidae, Proceratiinae) in China – with descriptions of three new species based on micro-CT enhanced next-generation-morphology

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