A dataset for earthworm communities in French Guiana
DOI:
https://doi.org/10.25674/414Keywords:
Oligochaeta, tropical rainforest, COI barcodes, alpha diversity, beta diversityAbstract
Earthworms represent a crucial taxon in soil ecosystems in terms of biomass and ecological functions. Knowledge of their diversity is growing, but the understanding of the ecological and evolutionary mechanisms underlying this diversity and its distribution patterns remains poorly understood. This is partly due to a lack of community data available on a large scale, particularly in the natural ecosystems of the most diverse tropical regions. Here we describe a large dataset containing records of 3555 georeferenced earthworm specimens, sampled in 125 one-hectare plots distributed in different habitats and localities across French Guiana. Each of these specimens was DNA barcoded targeting the cytochrome C Oxidase I subunit barcode region (COI), and these sequences were clustered into molecular operational taxonomic units (OTUs) that we used as species proxy to describe community taxonomic composition and diversity. Each community is associated in the dataset with climate and elevation data, and soil properties are also available for part of them. This dataset represents a unique opportunity for analyzing community diversity and phylogeographic patterns in neotropical rainforests.
References
Anthony, M. A., S. F. Bender & M. G. A. van der Heijden (2023): Enumerating soil biodiversity. – Proceedings of the National Academy of Sciences 120: e2304663120 [https://doi.org.inee.bib.cnrs.fr/10.1073/pnas.2304663120].
Bartz, M. L. C., G. G. Brown, M. G. Da Rosa, O. K. Filho, S. W. James, T. Decaëns & D. Baretta (2014): Earthworm richness in land-use systems in Santa Catarina, Brazil. – Applied Soil Ecology 83: 59–70 [https://doi.org/10.1016/j.apsoil.2014.03.003].
Baselga, A., D. Orme, S. Villeger, J. De Bartoli, F. Leprieur (2018): betapart: Partitioning Beta Diversity into Turnover and Nestedness Components. R package version 1.5.1.
Boyer, F., C. Mercier, A. Bonin, Y. Le Bras, P. Taberlet & E. Coissac (2016): OBITOOLS: a UNIX-inspired software package for DNA metabarcoding. – Molecular Ecology Resources 16: 176–182 [https://doi.org/10.1111/1755-0998.12428].
Cameron, E. K., I. S. Martins, P. Lavelle, J. Mathieu, L. Tedersoo, F. Gottschall, C. A. Guerra, J. Hines, G. Patoine, J. Siebert & et al. (2018): Global gaps in soil biodiversity data. – Nature Ecology & Evolution 2: 1042–1043 [https://doi.org/10.1038/s41559-018-0573-8].
Capowiez, Y., D. Marchán, T. Decaëns, M. Hedde & N. Bottinelli (2024): Let earthworms be functional – Definition of new functional groups based on their bioturbation behavior. – Soil Biology and Biochemistry 188: 109209 [https://doi.org/10.101/j.soilbio.2023.109209].
Decaëns, T., J. J. Jiménez, C. Gioia, J. Measey, P. Lavelle (2006): The values of soil animals for conservation biology. – European Journal of Soil Biology 42: S23–S38 [https://doi.org/10.1016/j.ejsobi.2006.07.001].
Decaëns, T. (2010): Macroecological patterns in soil communities. – Global Ecology and Biogeography 19: 287–302 [https://doi.org.inee.bib.cnrs.fr/10.1111/j.1466-8238.2009.00517.x].
Decaëns, T., D. Porco, R. Rougerie, G. G. Brown & S. W. James (2013): Potential of DNA barcoding for earthworm research in taxonomy and ecology. – Applied Soil Ecology 65: 35–42 [https://doi.org/10.1016/j.apsoil.2013.01.001].
Decaëns, T., D. Porco, S. W. James, G. G. Brown, V. Chassany, F. Dubs, L. Dupont, E. Lapied, R. Rougerie, J.-P. Rossi & et al. (2016): DNA barcoding reveals diversity patterns of earthworm communities in remote tropical forests of French Guiana. – Soil Biology and Biochemistry 92: 171– 183 [https://doi.org/10.1016/j.soilbio.2015.10.009].
Decaëns, T., M. C. Bartz, A. M. Feijo, A. Goulpeau, E. Lapied, D. F. Marchán, M. E. Maggia, G. Papuga & S. W. James (2024): Earthworms (Oligochaeta, Clitellata) of the Mitaraka range, French Guiana: commented checklist with description of one genus and eighteen species new to science. – Zoosystema 46(9): 195–244 [https://doi.org/10.5252/zoosystema2024v46a9].
Edgar, R. C. (2004): MUSCLE: multiple sequence alignment with high accuracy and high throughput. – Nucleic Acids Research 32: 1792–1797 [https://doi.org/10.1093/nar/gkh340].
Eisenhauer, N. (2010): The action of an animal ecosystem engineer: Identification of the main mechanisms of earthworm impacts on soil microarthropods. – Pedobiologia 53: 343–352 [https://doi.org/10.1016/j.pedobi.2010.04.003].
Folmer, O., M. Black, W. Hoeh, R. Lutz & R. Vrijenhoek (1994): DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. – Molecular Marine Biology and Biotechnology 3: 294–299.
Goulpeau, A., B. Penel, M.-E. Maggia, D. F. Marchán, D. Steinke, M. Hedde & T. Decaëns (2022): OTU delimitation with earthworm DNA barcodes: a comparison of methods. – Diversity 14: 866 [https://doi.org/10.3390/d14100866].
Guerra, C. A., A. Heintz-Buschart, J. Sikorski, A. Chatzinotas, N. Guerrero-Ramirez, S. Cesarz, L. Beaumelle, M. C. Rillig, F. T. Maestre, M. Delgado-Baquerizo & et al. (2020): Blind spots in global soil biodiversity and ecosystem function research. – Nature Communications 11: 3870 [https://doi.org/10.1038/s41467-020-17688-2].
Hajibabaei, M., D. H. Janzen, J. M. Burns, W. Hallwachs & P. D. N. Hebert (2006): DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences – 103: 968–971 [https://doi.org/10.1073/pnas.0510466103].
Hebert, P. D. N., E. H. Penton, J. M. Burns, D. H. Janzen & W. Hallwachs (2004): Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. – Proceedings of the National Academy of Sciences 101: 14812–14817 [https://doi.org/10.1073/pnas.0406166101].
Hsieh, T. C., K. H. Ma & A. Chao (2019): iNEXT: iNterpolation and EXTrapolation for species diversity. R package version 2.0.19.
Kimura, M. (1980): A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. – Journal of Molecular Evolution 16: 111–120 [https://doi.org/10.1007/BF01731581].
Larsson, J. (2024): eulerr: area-proportional Euler and Venn diagrams with ellipses. R package version 7.0.1.
Lavelle, P., A. Spain, M. Blouin, G. G. Brown, T. Decaëns, M. Grimaldi, J. J. Jiménez, D. McKey, J. Mathieu, E. Velasquez & et al. (2016): Ecosystem engineers in a self-organized soil: A review of concepts and future research questions. – Soil Science 18: 91–109 [https://doi.org/10.1097/SS.0000000000000155].
Letunic, I. & P. Bork (2007): Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. – Bioinformatics 23: 127–128 [https://doi.org/10.1093/bioinformatics/btl529].
Maggia, M.-E., T. Decaëns, E. Lapied, L. Dupont, V. Roy, H. Schimann, J. Orivel, J. Murienne, C. Baraloto, K. Cottenie & et al. (2021): At each site its diversity: DNA barcoding reveals remarkable earthworm diversity in neotropical rainforests of French Guiana. – Applied Soil Ecology 164: 103932 [https://doi.org/10.1016/j.apsoil.2021.103932].
Puillandre, N., S. Brouillet & G. Achaz (2021): ASAP: Assemble species by automatic partitioning. – Molecular Ecology Resources 21: 609–620 [https://doi.org/10.1111/1755-0998.13281].
R Core Team (2023): R: A language and environment for statistical computing. Version 4.3.1. Richard, B., T. Decaëns, R. Rougerie, S. W. James, D. Porco, P. D. N. Hebert (2010): Re-integrating earthworm juveniles into soil biodiversity studies: species identification through DNA barcoding. – Molecular Ecology Resources 10: 606–614 [https://doi.org/10.1111/j.1755-0998.2009.02822.x].
Saitou, N. & M. Nei (1987): The neighbor-joining method: a new method for reconstructing phylogenetic trees. – Molecular Biology and Evolution 4: 406–425 [https://doi.org/10.1093/oxfordjournals.molbev.a040454].
Schloerke, B., D. Cook, J. Larmarange, F. Briatte, M. Marbach, E. Thoen, A. Elberg & J. Crowley (2024): GGally: Extension to ’ggplot2’. R package version 2.2.1.
Tamura, K., G. Stecher & S. Kumar, S. (2021): MEGA11: Molecular Evolutionary Genetics Analysis Version 11. – Molecular Biology and Evolution 38: 3022–3027 [https://doi.org/10.1093/molbev/msab120].
Touroult, J., M. Pollet & O. Pascal (2018): Overview of Mitaraka survey: research frame, study site and field protocols. – Zoosystema 40: 327–365 [https://doi.org/10.5252/zoosystema2018v40a13].
Whittaker, R. H. (1972): Evolution and measurement of species diversity. – Taxon 21: 213–251 [https://doi.org/10.2307/1218190].
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