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Methods and recommendations

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Archilegt edited this page Apr 26, 2024 · 78 revisions

Currently a dump list on methods and recommendations related to research on Myriapoda and Onychophora. This list may or may not end organized similarly to the sections of a scientific publication.

Acknowledgements:
M. Sc. Leif Moritz contributed information on repositories for morphological data and images in 2021. M. Sc. Giovanni Bianco (Senckenberg Gesellschaft für Naturforschung, Frankfurt) contributed two references on tree-related microhabitats (Bütler et al., 2020; Martin et al., 2022) in 2023.

Last updated: 26.iv.2024

Title

The title should fit the paper like a glove to a hand. Don't make the title too broad. If you are dealing with a subgenus, then write e.g., Otostigmus (Otostigmus) and not just Otostigmus.

Authorship

CRediT (Contributor Roles Taxonomy) is a high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to research outputs. The roles describe each contributor’s specific contribution to the scholarly output.
Website: https://credit.niso.org/

Abstract

Full scientific names of new taxa should be mentioned in the abstract, including authorship. This is very important for paywalled articles, of which the abstract is often all that one sees. Another reason to explicitly mention authorship of new taxa is when scientific name authorship is different from the authorship of the work in which the taxa are published.

Sampling area, geography, habitats, microhabitats, related standardized vocabularies

IUCN Global Ecosystem Typology
The IUCN Global Ecosystem Typology comprises six hierarchical levels. The three upper levels – realms, functional biomes and ecosystem functional groups – classify ecosystems based on their functional characteristics. The three lower levels – biogeographic ecotypes, global ecosystem types and subglobal ecosystem types – are often already in use and incorporated into policy infrastructure at national levels and can be linked to these upper levels. This is crucial, as important conservation action occurs at local levels, where most ecosystem-specific knowledge and data reside.
Website: https://global-ecosystems.org/
Press release: https://www.iucn.org/story/202210/iucn-global-ecosystem-typology-closes-major-gap-our-ability-measure-state-nature

Geographic distribution
Brummitt R. K. (2001): World Geographic Scheme for Recording Plant Distributions, Edition 2. Hunt Institute for Botanical Documentation, Carnegie Mellon University (Pittsburgh). http://rs.tdwg.org/wgsrpd/doc/data/

Country Codes
https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
ISO 3166-1 alpha-2 codes are two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to represent countries, dependent territories, and special areas of geographical interest.

Habitats
EUNIS habitat classification and the EU Habitats Directive Annex I habitat types
https://eunis.eea.europa.eu/habitats.jsp

Tree-related microhabitats

Geographical Thesauri

Getty Thesaurus of Geographic Names
https://www.getty.edu/research/tools/vocabularies/tgn/index.html
TGN is a thesaurus. TGN is not comprehensive. TGN is intended to aid cataloging, research, and discovery of information about visual works and related topics. The focus of TGN is on historical places, although enough information about the modern world is included to give context to historical places and to allow documenation and discovery of visual works. While most records in TGN include coordinates, these coordinates are approximate and are intended for reference ("finding purposes") only. The Getty Vocabularies are constructed to allow their use as Linked Open Data (LOD).

GeoNames
https://www.geonames.org/
The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.

Collecting methods

This section is organized from the highest above-ground sampling methods (e.g., forest canopy methods) to the deepest below-ground sampling methods. Both efficient and non-efficient collecting methods will be referred below.

Arboreal arthropod collector
A new active sampling technique combining the use of beating trays with a telescopic pole was proposed by Viana‐Junior et al. (2021). However, out of 8 888 arthropod specimens only one scutigeromorph was collected.
Viana‐Junior, A.B., Quijano‐Cuervo, L.G., Ferreira, J.C., do Nascimento Reis, R.R., dos Santos, I.A. and Martins, M.B. (2021): Collecting arboreal arthropods: a technique for sampling plant‐inhabiting arthropod communities in a tropical forest understory. Entomologia Experimentalis et Applicata, 169: 312-321. https://doi.org/10.1111/eea.13012

Branch trap for canopy arthropods
A new interception + fall trap designed for sampling arthropods on thick tree branches was proposed by Koponen et al. (1997). It was successful at sampling several invertebrate groups, including Diplopoda and Chilopoda.
Koponen, S., Rinne, V., and Clayhills, T. (1997): Arthropods on oak branches in SW Finland, collected by a new trap type. Entomologica Fennica, 8 (3): 177–183. https://doi.org/10.33338/ef.83940

Malaise traps
In general, not efficient for sampling myriapods.
Michael J Skvarla, Jonathan L Larson, J Ray Fisher, Ashley P G Dowling (2020): A Review of Terrestrial and Canopy Malaise Traps. Annals of the Entomological Society of America, 114 (1): 27–47. https://doi.org/10.1093/aesa/saaa044
Remark: Chilopoda and Diplopoda, as per reference to Moeed & Meads (1987), were overlooked on table 4, page 34.
Abdul Moeed & M. J. Meads (1987): Seasonality of arthropods caught in a Malaise trap in mixed lowland forest of the Orongorongo Valley, New Zealand. New Zealand Journal of Zoology, 14 (2): 197-208. https://doi.org/10.1080/03014223.1987.10422990

Pitfall traps
Efficient for sampling myriapods.
Stašiov, S., Čiliak, M., Wiezik, M., Svitok, M., Wieziková, A., & Diviaková, A. (2021). Pitfall trap design affects the capture efficiency of harvestmen (Opiliones) and millipedes (Diplopoda). Ecology and Evolution, 11 (14): 9864– 9875. https://doi.org/10.1002/ece3.7820

Preparation techniques

For preservation

For examination - Holding

  • Wanke, D., Bigalk, S., Krogmann, L., Wendt, I., Rajaei, H. (2019): The Fixator—A simple method for mounting of arthropod specimens and photography of complex structures in liquid. Zootaxa, 4657 (2): 385-391. https://doi.org/10.11646/zootaxa.4657.2.11
  • Wanke, D., Ulmer, J. H., Wendt, I., Rajaei, H. (2021): Updates on the Fixator—Facilitating the investigation, mounting, and photography of structures and specimens in liquid. Zootaxa, 4999 (4): 397-400. https://doi.org/10.11646/zootaxa.4999.4.9
  • SEM specimen holder, see Pohl H. (2010): A scanning electron microscopy specimen holder for viewing different angles of a single specimen. Microscopy Research and Technique, 73 (12): 1073-1076. https://doi.org/10.1002/jemt.20835

For examination - Embedding

  • Hüther mixture: An embedding medium developed by Hüther, W. (1993): Sammel- und Präparationsmethoden für Bodenarthropoden. Abhandlungen und Berichte des Naturkundemuseums Görlitz, 66 (6): 1-11.

Standardized terminology

Morphology - Onychophora
Morphological descriptive nomenclature for Onychophora can follow Read (1988), Storch & Ruhberg (1993), and Oliveira et al. (2010).

  • Read, V. M. S. J. (1988). The application of scanning electron microscopy to the systematics of the neotropical Peripatidae (Onychophora). Zoological Journal of the Linnean Society, 93, 187–223.
  • Storch, V., and H. Ruhberg. 1993. Onychophora. In F.W. Harrison and M.E. Rice (editors), Microscopic anatomy of invertebrates, vol. 12, Onychophora, Chilopoda, and lesser Protostomata: 11–56. New York: Wiley.
  • Oliveira, I. S., Wieloch, A. H., & Mayer, G. (2010). Revised taxonomy and redescription of two species of the Peripatidae (Onychophora) from Brazil: A step towards consistent terminology of morphological characters. Zootaxa, 2493, 16–34.

Morphology - Chilopoda

  • Bonato L, Edgecombe G, Lewis J, Minelli A, Pereira L, Shelley R, Zapparoli M (2010): A common terminology for the external anatomy of centipedes (Chilopoda). ZooKeys, 69: 17-51. https://doi.org/10.3897/zookeys.69.737

Morphology - Diplopoda

  • Hopkin, S. P, & H. J. Read. 1992. The Biology of Millipedes. Oxford University Press, New York, 232 pp. [The terminology for mouthparts has been reused]
  • Keeton, W. T. 1960. A taxonomic study of the milliped family Spirobolidae (Diplopoda: Spirobolida). Memoirs of the American Entomological Society, 17: 1-146. [The terminology for genitalic structures has been reused]
  • Kohler, H. R., & G. Alberti. 1991. Morphology of the mandibles in millipedes (Diplopoda, Arthropoda). Zoologica Scripta, 19: 195-202. [The terminology for mouthparts has been reused]

Color description
Coloration description from photographs of living specimens can follow the standard names of the 267 Color Centroids of the NBS/ISCC Color System. See Centore (2016) and Kelly (1958), implemented by Costa & Giribet (2021).

  • Centore, P. (2016). sRGB centroids for the ISCC-NBS colour system. https://www.munsellcolourscienceforpa inters.com/ColourSciencePapers/sRGBCentroidsForTheISCCNBSColourSystem.pdf
  • Kelly, K. L. (1958). Central notations for the revised ISCC-NBS color-name blocks. Journal of Research of the National Bureau of Standards, 61, 427–431.
  • Costa, C. S., & Giribet, G. (2021). Panamanian velvet worms in the genus Epiperipatus, with notes on their taxonomy and distribution and the description of a new species (Onychophora, Peripatidae). Invertebrate Biology, 140 (3), e12336. https://doi.org/10.1111/ivb.12336

Klaer lightende spiegel der verjkonst...
A treaty on colors from 1692
bibliotheque-numerique.citedulivre-aix.com/idviewer/35315/1
https://www.thisiscolossal.com/2014/05/color-book/

Werner's nomenclature of colours
https://archive.org/details/gri_c00033125012743312

Codes for the Representation of Names of Languages
https://www.loc.gov/standards/iso639-2/php/code_list.php

International System of Units
International Bureau of Weights and Measures (2019): The International System of Units (SI) (9th ed.). ISBN 978-92-822-2272-0. https://www.bipm.org/documents/20126/41483022/SI-Brochure-9.pdf
See also: International System of Units in Wikipedia

Standardized measurement of functional traits
Moretti, M., Dias, A.T.C., de Bello, F., Altermatt, F., Chown, S.L., Azcárate, F.M., Bell, J.R., Fournier, B., Hedde, M., Hortal, J., Ibanez, S., Öckinger, E., Sousa, J.P., Ellers, J. and Berg, M.P. (2016): Handbook of protocols for standardized measurement of terrestrial invertebrate functional traits. Functional Ecology, 31 (3): 558-567. https://doi.org/10.1111/1365-2435.12776

Native/invasive species
Lemoine, R.T. and Svenning, J.-C. (2022): Nativeness is not binary—a graduated terminology for native and non-native species in the Anthropocene. Restor Ecol, 30: e13636. https://doi.org/10.1111/rec.13636

Taxonomic identification

Validation of taxonomic identifications and correctly citing associated literature, with recommendations to authors, reviewers, and editors:

  • Meier, R. (2017): Citation of taxonomic publications: the why, when, what and what not. Systematic Entomology, 42: 301-304. https://doi.org/10.1111/syen.12215
  • Packer, L., Monckton, S.K., Onuferko, T.M. and Ferrari, R.R. (2018): Validating taxonomic identifications in entomological research. Insect Conservation and Diversity, 11: 1-12. https://doi.org/10.1111/icad.12284
  • Simon, C. (2018): Correct procedure for citing taxonomic works in non-taxonomic scientific papers. African Zoology, 53:3, i-ii. https://doi.org/10.1080/15627020.2018.1532138
  • Monckton, S.K., Johal, S. and Packer, L. (2020): Inadequate treatment of taxonomic information prevents replicability of most zoological research. Canadian Journal of Zoology, 98(9): 633-642. https://doi.org/10.1139/cjz-2020-0027

Open Nomenclature
"Open Nomenclature" and "Open Nomenclature qualifiers" refer to terms like sensu stricto, sensu lato, cf., aff., and so on. CAMM compiled a list of sources on the topic, including scientific articles, a handout, and two wikis, which were submitted to EUdaphobase as part of the documentation for implementing and standardising ON qualifiers:

Building taxonomic keys
Walter, D. E. and Shaun Winterton (2006): Keys and the Crisis in Taxonomy: Extinction or Reinvention? Annual Review of Entomology, 52 (1): 193-208. https://doi.org/10.1146/annurev.ento.51.110104.151054

Illustrations, design, and editing

Phylopic - Free silhouette images of animals, plants, and other life forms.
Anyone may contribute. Available for reuse under a Public Domain or Creative Commons license. Website by T. Michael Keesey.
http://phylopic.org/
See:
Onychophora: http://phylopic.org/name/f2152a9e-07dc-451f-850c-11d42602be39
Myriapoda: http://phylopic.org/name/5ed41805-2d55-4107-9edb-cc6099ba906d
No Euthycarcinoidea as of 22.xi.2022.

SankeyMATIC - A Sankey diagram builder for everyone (http://sankeymatic.com/)
Bik HM, Pitch Interactive. Phinch: An interactive, exploratory data visualization framework for—Omic datasets. bioRxiv. 2014. https://doi.org/10.1101/009944

GNU Image Manipulation Program - GIMP (https://www.gimp.org)
GIMP is a cross-platform image editor available for GNU/Linux, macOS, Windows and more operating systems. It is free software, its source code can be changed and the changes distributed.
Example of use: Editing scanning electron microscope images for publication. Image cropping, correction of tones, background editing. Used by myriapodologist William Shear.

Inkscape: Draw Freely (https://inkscape.org)
Inkscape is professional quality vector graphics software which runs on Linux, Mac OS X and Windows desktop computers.

Image to map calibration tool:
Cartograph Maps 3.1.3 and newer ships with a raster image calibration tool which creates maps from raster images, such as photos or scans from maps. https://www.cartograph.eu/v3/image-to-map-calibration-tool/

Data cleaning

OpenRefine (previously Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.
https://openrefine.org/

Molecular methods and software

  • Patzold F, Zilli A, Hundsdoerfer AK (2020): Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLOS ONE 15(7): e0235222. https://doi.org/10.1371/journal.pone.0235222
  • Ribeiro CVR, Oliveira LP, Batista R, De Sousa M (2021): UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs). Biodiversity Data Journal, 9: e78132. https://doi.org/10.3897/BDJ.9.e78132

Species delimitation

Data repositories

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008): GenBank. Nucleic Acids Research, 36 (Issue suppl_1): D25-D30. https://doi.org/10.1093/nar/gkm929
  • Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2012): GenBank. Nucleic Acids Research, 41 (Issue D1): D36–D42. https://doi.org/10.1093/nar/gks1195
  • European Organization For Nuclear Research, OpenAIRE (2013): Zenodo. https://doi.org/10.25495/7gxk-rd71 [All-purpose repository]
  • Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Tadler MS, Weibulat T, Wilke T, Renner SS, Vences M (2020): Repositories for Taxonomic Data: Where We Are and What is Missing, Systematic Biology, 69 (6): 1231–1253. https://doi.org/10.1093/sysbio/syaa026
  • Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017): Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes, 3: e12431. https://doi.org/10.3897/rio.3.e12431
  • Ratnasingham S, Hebert PDN (2007): BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes, 7 (3): 355–364. https://doi.org/10.1111/j.1471-8286.2006.01678.x

The morphological data repositories can be used to upload images (e.g., photographs, videos, SEMs, µCt data) or 3D data (e.g., segmentations), and also tables (e.g., character matrices, measurements etc.). The data can be linked to taxa or specimens in collections. It can be images that are already printed in the article but also additional or supplementary data (e.g., when you have taken more photographs or SEMs than you actually publish in an article).
Example from Morphobank on how such a repository can store CT-data and histological data:
Project 3582: L. Moritz, M. Koch. 2020. No Tömösváry organ in flat backed millipedes (Diplopoda, Polydesmida). ZooKeys. 930:103-115. https://doi.org/10.7934/P3582

Citing software and datasets

Semantic Versioning 2.0.0

https://semver.org/#semantic-versioning-200

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