Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Luca Gregnanin (gr.luca96@gmail.com)
Academic editor: Stylianos Simaiakis
Received: 02 Mar 2024 | Accepted: 28 Mar 2024 | Published: 21 May 2024
© 2024 Luca Gregnanin, Lucio Bonato
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Gregnanin L, Bonato L (2024) A comprehensive dataset of the geophilid centipedes of the south-eastern Alps (Chilopoda, Geophilomorpha, Geophilidae s.l.). Biodiversity Data Journal 12: e122144. https://doi.org/10.3897/BDJ.12.e122144
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Centipedes of the family Geophilidae s.l. are widespread in the Holarctic, with the south-eastern part of the European Alps standing out as one of the most investigated regions. However, retrieving the published records for this taxon, even for this region, is challenging, since most of them are sparse in the specialised literature and interpreting them is hampered by the many taxonomic and nomenclatorial changes occurred in the past and recent times.
We assembled and released a dataset of occurrence records of the geophilid species in the south-eastern Alps, including all the published records and many other records present in unpublished catalogues of scientific collections. For each record, we integrated information from all the sources about: locality, date of collection, the taxonomic identifications, number and sex of individuals and available sequences of molecular markers. For all the records, we estimated geographic coordinates of the locality, when not originally provided, based on the information available. We also estimated the accuracy of the position.
The dataset includes 3293 records referred to 39 species, obtained since the first half of the 19th century and up to 2022; 52% of these records have been released publicly for the first time in the dataset here described.
Geophilidae, Chilopoda, south-eastern Alps, georeferenced dataset, records, Darwin Core
The Geophilidae s.l. is a large lineage of centipedes mainly found throughout the Holarctic with nearly 700 recognised species, some of them traditionally separated in different families (
The diversity of geophilids has been studied to varying degrees in different regions. The south-eastern part of the European Alps stands out as one of the most intensely investigated regions. Here, the earliest published records of geophilids date back to the 19th century (e.g.,
However, even within this region, the taxonomy of some groups of species is still imprecise and most probably inaccurate and the actual number of species remains to be clarified (e.g., in the genera Geophilus and Stenotaenia;
Most of the published information about the presence, distribution and ecology of geophilids in the south-eastern Alps is scattered throughout many national or regional journals, in many cases difficult to retrieve, because they are not indexed in modern digital bibliographic catalogues and are not yet available in public digital archives. Indeed, in the last decades, a few synoptic works, with broader taxonomic and geographic scopes, summarised the published records of geophilids species in the south-eastern Alps, providing textual lists of new occurrence records (
Here, we present a comprehensive, updated and newly-georeferenced dataset of occurrence records of Geophilidae s.l. from the south-eastern Alps. It includes all the published records, to the best of our knowledge, and many other records retrieved from the catalogues of many major scientific collections hosting relevant specimens (either unpublished catalogues or catalogues available online). For each record, we provided information on locality, date, collector/s, number of individuals recorded, their sex, habitat in which the animals were found and identifiers of published genetic sequences. On top of the original identification, we provided also the different identifications published in subsequent sources and the valid scientific name (according to the taxonomy currently in use) for the species to which each record was assigned in its latest citation.
A comprehensive dataset of the geophilid centipedes of the south-eastern Alps (Chilopoda, Geophilomorpha, Geophilidae s.l.)
Luca Gregnanin, Lucio Bonato.
The study area (Fig.
South-eastern part of the European Alps. For further details, see "Study area description".
45.1287 and 46.9219 Latitude; 15.8613 and 9.9074 Longitude.
Geophilidae Leach, 1816, sensu
Rank | Scientific Name |
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superclass | Myriapoda |
class | Chilopoda |
order | Geophilomorpha |
family | Geophilidae Leach, 1816 |
genus | Acanthogeophilus Minelli, 1982 |
genus | Clinopodes C.L. Koch, 1847 |
genus | Dignathodon Meinert, 1870 |
genus | Eurygeophilus Verhoeff, 1899 |
genus | Geophilus Leach, 1814 |
genus | Henia C.L. Koch, 1847 |
genus | Pachymerium C.L. Koch, 1847 |
genus | Pleurogeophilus Verhoeff, 1901 |
genus | Stenotaenia C.L. Koch, 1847 |
genus | Strigamia Gray, 1843 |
species | Clinopodes carinthiacus (Latzel, 1880) |
species | Clinopodes flavidus C.L. Koch, 1847 |
species | Clinopodes rodnaensis (Verhoeff, 1938) |
species | Clinopodes strasseri (Verhoeff, 1938) |
species | Clinopodes vesubiensis Bonato, Iorio & Minelli, 2011 |
species | Dignathodon microcephalus (Lucas, 1846) |
species | Eurygeophilus pinguis (Brölemann, 1898) |
species | Geophilus carnicus Verhoeff, 1928 |
species | Geophilus carpophagus Leach, 1815 |
species | Geophilus electricus (Linnaeus,1758) |
species | Geophilus flavus (De Geer, 1778) |
species | Geophilus impressus C.L. Koch, 1847 |
species | Geophilus labrofissus Verhoeff, 1938 |
species | Geophilus minimus Verhoeff, 1928 |
species | Geophilus oligopus (Attems, 1895) |
species | Geophilus piae Minelli, 1983 |
species | Geophilus proximus C.L. Koch, 1847 |
species | Geophilus pusillifrater Verhoeff, 1898 |
species | Geophilus pygmaeus Latzel, 1880 |
species | Geophilus truncorum Bergsøe & Meinert, 1866 |
species | Henia bicarinata (Meinert, 1870) |
species | Henia brevis (Silvestri, 1896) |
species | Henia illyrica (Meinert, 1870) |
species | Henia montana (Meinert, 1870) |
species | Henia vesuviana (Newport, 1845) |
species | Pachymerium ferrugineum (C.L. Koch, 1835) |
kingdom | Pleurogeophilus mediterraneus (Meinert, 1870) |
species | Stenotaenia linearis (C.L. Koch, 1835) |
species | Stenotaenia romana (Silvestri, 1895) |
species | Stenotaenia sorrentina (Attems, 1903) |
species | Strigamia acuminata (Leach, 1816) |
species | Strigamia carniolensis (Verhoeff, 1895) |
species | Strigamia crassipes (C.L. Koch, 1835) |
species | Strigamia engadina (Verhoeff, 1935) |
This work is licensed under a Creative Commons Attribution (CC-BY 4.0) Licence.
Column label | Column description |
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occurrenceID | An identifier for the dwc:Occurrence (as opposed to a particular digital record of the dwc:Occurrence). Value: a text in the format "R####" (#: 0-9). |
basisOfRecord | The specific nature of the data record. Value: "MaterialCitation", "PreservedSpecimen". |
ownerInstitutionCode | The name in use by the institution (reported as) having ownership of the object(s) or information referred to in the record. Value: a text. |
collectionCode | The name identifying the collection from which the record was derived. Value: a text. |
catalogNumber | An identifier for the record within the data set or collection. Value: a text. |
recordedBy | A list (concatenated and separated) of names of people responsible for recording the original dwc:Occurrence. Value: a list separated by " | ", including the surname and the first letter of the name (when known) of each person; ordered alphabetically. |
occurrenceRemarks | Comments or notes about the dwc:Occurrence. Value: a text. |
eventDate | The date-time or interval during which a dwc:Event occurred. For occurrences, this is the date-time when the dwc:Event was recorded. Value: a date or time interval conforming ISO 8601-1:2019. |
eventRemarks | Comments or notes about the dwc:Event. Value: a possible eventDate for the dwc:Event. |
higherGeography | A geographic name less specific than the information captured in the dwc:locality term. Value: the name of the alpine "section" according to the SOIUSA partition of the Alps, preceded by "near" for the records falling outside the conventional borders of the section. |
verbatimLocality | The original textual description of the place. Value: a text. |
locality | The specific description of the place. Value: the current name of the locality in the main national language(s) of the country to which the locality belongs. |
decimalLatitude | The geographic latitude (in decimal degrees, using the spatial reference system WGS84) of the geographic center of a dcterms:Location. Value: a number. |
decimalLongitude | The geographic longitude (in decimal degrees, using the spatial reference system WGS84) of the geographic center of a dcterms:Location. Value: a number. |
geodeticDatum | The spatial reference system (SRS) upon which the geographic coordinates given in dwc:decimalLatitude and dwc:decimalLongitude are based. Value: for all the records with geographic coordinates, "WGS84". |
coordinateUncertaintyInMeteres | The horizontal distance (in meters) from the given dwc:decimalLatitude and dwc:decimalLongitude describing the smallest circle containing the whole of the dcterms:Location. Value: a number. |
georeferenceRemarks | Notes or comments about the spatial description determination. Value: a text. |
minimumElevationInMeteres | The lower limit of the range of elevation (altitude, usually above sea level), in meters. Value: a number. |
maximumElevationInMeteres | The upper limit of the range of elevation (altitude, usually above sea level), in meters. Value: a number. |
habitat | A category or description of the habitat in which the dwc:Event occurred. Value: names of plant genera or species, names of phytosociological entities, or other. |
verbatimIdentification | A string representing the taxonomic identification as it appeared in the original record. Value: text. |
identifiedBy | A list (concatenated and separated) of names of people who assigned the dwc:Taxon to the subject. Value: a list separated by " | ", including the surname and the first letter of the name (when known) of each person; ordered alphabetically; only reported for unpublished records. |
dateIdentified | The date on which the subject was determined as representing the dwc:Taxon. Value: a date or time interval conforming ISO 8601-1:2019; only reported for unpublished records. |
scientificName | The full scientific name, with authorship and date information. Value: the taxonomic name currently considered valid for the taxon indicated in the verbatimIdentification or for the taxon under which the record was identified in its last citation. |
taxonRank | The taxonomic rank of the most specific name in the dwc:scientificName. Value: "family", "genus", "species". |
identificationRemarks | Comments or notes about the dwc:Identification. Value: a text. |
taxonRemarks | Comments or notes about the taxon or name. Value: a text. |
identificationQualifier | A brief phrase or a standard term ("cf.", "aff.") to express the doubts about the dwc:scientificName. Value: "cf.". |
individualCount | The number of individuals present at the time of the dwc:Occurrence. Value: a number. |
sex | The sex of the biological individual(s) represented in the dwc:Occurrence. Value: "male", "female", their concatenation through " | ". |
organismRemarks | Comments or notes about the dwc:Organism instance. Value: possible individualCount for the dwc:Organism. Value: a text. |
associatedReferences | A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the dwc:Occurrence. Value: a list separated by " | " of complete citations of all the published sources citing the record; ordered chronologically. |
dynamicProperties | A list of additional or amending identifications, dates and localities provided in publications other than the original source. Value: a key:value pair dictionary with keys including author-date references cited in dwc:associatedReferences and values including the additional or amending information. |
associatedSequences | A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the dwc:MaterialEntity. Value: a structured text: "marker: [list separated by " | " of GenBank urls]. |
For our purpose, a record was intended as any report of the finding of one or more individuals of a species in a single location and in a single day.
We searched for all the original records of Geophilidae s.l. in the study area browsing the whole scientific literature reporting records of Chilopoda published up to 2023, however ignoring graduation theses. We also gathered records from the digital catalogues of the major scientific collections of research institutions known to host relevant myriapodological collections and expected to include specimens from the study area: the "Chilobio" centipede collection of the Animal Ecology Group, University of Ljubljana (
The "original source" of a record was intended as the earliest publication reporting the record, if any.
Records were included in the dataset when they were accompanied by at least an indication of the locality (e.g., textual indications, codes of geographical units or geographic coordinates) and a taxonomic identification at the genus level or more precise.
Additional information digitised for each record included any indication, either published in the original source or available from other sources on: time of the recording event (e.g., date, period), habitat (e.g., phytosociological entities, names of plant genera or species type of soil), number and sex of the individuals and the GenBank urls of the available sequences of the main molecular markers employed in molecular taxonomy, phylogeography and population genetics of centipedes, namely the "barcode fragment" of COI, the 16S, 18S and 28S markers, obtained from collected specimens associated with the record. We also queried the BOLD and GenBank databases for additional sequences.
For the name and the structure of the columns of the dataset, we followed the Darwin Core standard (
For each record, the locality where the animals were found was reported as spelled in the original source (in the column "verbatimLocality). A name of the locality was also provided in the main official language(s) of the country to which the locality belongs (in the column "locality"). These latter names were searched in institutional sources (e.g., websites of local administrative institutions) and in topographic maps (e.g., for Italy, the "Carta Topografica d'Italia" map at the scale 1:25000, available as a Web Map Service at http://wms.pcn.minambiente.it/ogc?map=/ms_ogc/ WMS_v1.3/raster/IGM_25000.map).
For each record, the georeferencing of the locality was reported following the "point-radius" method (
For each record, we reported the taxonomic name used in the original source (in the column "verbatimIdentification"), other names used for the record in subsequent publications (in the column "dynamicProperties"), and the name currently considered valid for the most recent identification (in the column "scientificName").
For the scientificName, we followed the "Checklist of the Italian Fauna" (
We reported many records of Henia and Geophilus, attributed to four putative undescribed species in their original sources, as identified to the genus level in scientificName. They have been flagged with the provisional labels Henia sp.1, Geophilus sp.1, Geophilus sp. 2. and Geophilus sp.3 in the column "taxonRemarks".
The dataset includes 3293 records, based on about 7700 collected specimens. They are assigned to 39 species or species–species complexes of Geophilidae s.l., of which four putative species are still undescribed.
A total of 1595 records (48%) were already published, while the remaining 1698 are here released for the first time, being only found in unpublished catalogues of scientific collections. The already published records were found in 86 publications since 1847 (a complete list of references is available in Suppl. material
The geographic distribution of the records is heterogeneous (Fig.
Geographic distribution of the records. Each cell has an area of ~ 40 km2. The colour of each cell is associated with the number of records already published (increasing yellow intensity) and to the number of records not yet published (increasing blue intensity). Cells without colour have no records.
For 1830 records (56%), the uncertainty of the geographic coordinates was ≤ 500 m (Fig.
Frequency distribution of the uncertainty of the position of the records (only records with uncertainty < 100 km were georeferenced and are included in this plot). The inset illustrates the uncertainty of the coordinates of each record (records are arranged from the least to the most accurate on the x-axis; note the logarithmic scale on the y-axis).
The oldest record in the dataset dates to 1847 or before (
We are grateful to Nesrine Akkari (Naturhistorisches Museum Wien), Paolo Glerean (Museo Friulano di Storia Naturale, Udine), Ivan and Anja Kos (Animal Ecology Group, University of Ljubljana), Leonardo Latella and Roberta Salmaso (Museo di Storia Naturale, Verona), Monica Leonardi (Museo di Storia Naturale di Milano) and Paolo Pantini (Museo Civico di Scienze Naturali "E. Caffi", Bergamo) for providing us with the access to the digital catalogues of the collections under their supervision. We thank Emiliano Peretti and Roberto Magnolini for their suggestions and help in checking the records of some of the species.
We thank Robert Mesibov for his help and suggestions in the structure and cleaning of the dataset, and Stylianos Simaiakis and Ivan Hadrián Tuf, as reviewers of this paper, for their suggestions in the main text and supplementary material.
This research was supported by the Italian Ministry of University and Research (project funded by the European Union - Next Generation EU: “PNRR Missione 4 Componente 2, “Dalla ricerca all’impresa”, Investimento 1.4, Progetto CN00000033”).
The file includes all the references reporting original records included in the dataset or citing the records with new or amending information.