Abstract
Earthworms are a widespread and ecologically important group of animals, which has the highest total biomass in some ecosystems and often defines the composition of soil fauna. Earthworms are known to have high cryptic genetic diversity. In this study we attempted to estimate earthworm species diversity in the south of West Siberia by DNA barcoding. This method employs short fragments of the genome to identify species, and allows one to work with specimens that cannot be identified by conventional techniques, as well as to search for new species and predict their phylogenetic affinities. As the target sequence we took a fragment of the mitochondrial cytochrome oxidase 1 (cox1) gene. The studied territory (Novosibirsk and Tomsk oblasts, Altai krai, and the Altai Republic) is known to contain 16 species and subspecies of earthworms. We analyzed 259 individuals from twelve locations and detected 27 genetic clusters. Ten of them correspond to known species (A. caliginosa, E. fetida, O. tyrtaeum, D. rubidus tenuis, D. octaedra, E. balatonica, E. sibirica, as well as three genetic lineages ofE. nordenskioldi nordenskioldi). Seventeen of the 27 clusters do not have close sequence similarity to any known earthworm species. Representatives of some of these novel clusters are morphologically similar to the Eisenia n. nordenskioldi/E. n. pallida species complex and may belong to new genetic lineages of this complex. The rest of the novel clusters probably represent new earthworm species. Therefore, we can conclude that a large portion of earthworm biodiversity in the south of West Siberia is still unexplored.
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Bely, A.E. and Wray, G.A., Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase i, Mol. Phylogenet. Evol., 2004, vol. 30, pp. 50–63. doi 10.1016/S1055-7903(03)00180-5
Bienert, F., De Danieli, S., Miquel, C., Coissac, E., Poillot, C., and Brun, J.-J., Tracking earthworm communities from soil DNA, Mol. Ecol., 2012, vol. 21, no. 8, pp. 2017–2030. doi 10.1111/j.1365-294X.2011.05407.x
Birky, C.W., Jr., Adams, J., Gemmel, M., and Perry, J., Using population genetic theory and DNA sequences for species detection and identification in asexual organisms, PLoS One, 2010, vol. 5, no. 5, p. 10609. doi 10.1371/journal. pone.0010609
Buckley, T.R., James, S., Allwood, J., Bartlam, S., Howitt, R., and Prada, D., Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity, Mol. Phylogenet. Evol., 2011, vol. 58. doi 10.1016/j.ympev.2010.09.024
Chang, C.-H. and James, S., A critique of earthworm molecular phylogenetics, Pedobiologia, 2011, vol. 54, pp. S3–S9. doi 10.1016/j.pedobi.2011.07.015
Decaëns, T., Porco, D., Rougerie, R., Brown, G.G., and James, S.W., Potential of DNA barcoding for earthworm research in taxonomy and ecology, Appl. Soil Ecol., 2013, vol. 65, pp. 35–42. doi 10.1016/j.apsoil.2013.01.001
Fernández, R., Almodóvar, A., Novo, M., Simancas, B., and Díaz Cosín, D.J., Adding complexity to the complex: New insights into the phylogeny, diversification and origin of parthenogenesis in the Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae), Mol. Phylogen. Evol., 2012, vol. 64, no. 2, pp. 368–379. doi 10.1016/j.ympev.2012.04.011
Folmer, O., Black, M., Hoeh, W., Lutz, R., and Vrijenhoek, R., DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol. Mar. Biol. Biotech., 1994, vol. 3, pp. 294–299.
Giska, I., Sechi, P., and Babik, W., Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated, BMC Evol. Biol., 2015, vol. 15, p. 217. doi 10.1186/s12862-015-0488-9
Hebert, P.D.N., Ratnasingham, S., and de Waard, J.R., Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species, Proc. R. Soc. B, 2003, vol. 270, pp. 96–99. doi 10.1098/rsbl.2003.0025
Hendrix, P.F., Callaham, M.A., Drake, J.M., Huang, C.-Y., James, S.W., Snyder, B.A., and Zhang, W., Pandora’s box contained bait: The global problem of introduced earthworms, Ann. Rev. Ecol., Evol. Syst., 2008, vol. 39, pp. 593–613. doi 10.1146/annurev.ecolsys.39.110707.173426
James, S.W. and Davidson, S.K., Molecular phylogeny of earthworms (Annelida: Crassiclitellata) based on 28S, 18S and 16S gene sequences, Invertebr. Syst., 2012, vol. 26, pp. 213–229. doi 10.1071/IS11012
King, R.A., Tibble, A.L., and Symondson, W.O.C., Opening a can of worms: Unprecedented sympatric cryptic diversity within British lumbricid earthworms, Mol. Ecol., 2008, vol. 17, no. 21, pp. 4684–4698. doi 10.1111/j.1365- 294X.2008.03931.x
Pérez-Losada, M., Bloch, R., Breinholt, J.W., Pfenninger, M., and Domínguez, J., Taxonomic assessment of Lumbricidae (Oligochaeta) earthworm genera using DNA barcodes, Eur. J. Soil Biol., 2012, vol. 48, pp. 41–47. doi 10.1016/ j.ejsobi.2011.10.003
Pop, A.A., Cech, G., Wink, M., Csuzdi, C., and Pop, V.V., Application of 16S, 18S rDNA and COI sequences in the molecular systematics of the earthworm family Lumbricidae (Annelida, Oligochaeta), Eur. J. Soil Biol., 2007, vol. 43, pp. S43–S52. doi 10.1016/j.ejsobi.2007.08.007
Porco, D., Decaens, T., Deharveng, L., James, S.W., Skarzynski, D., Erséus, C., Butt, K.R., Richard, B., and Hebert, P.D.N., Biological invasions in soil: DNA barcoding as a monitoring tool in a multiple taxa survey targeting European earthworms and springtails in North America, Biol. Invasions, 2013, vol. 15, pp. 899–910. doi 10.1007/s10530-012-0338-2
Richard, B., Decaëns, T., Rougerie, R., James, S.W., Porco, D., and Hebert, P.D.N., Re-integrating earthworm juveniles into soil biodiversity studies: Species identification through DNA barcoding, Mol. Ecol. Res., 2010, vol. 10, no. 4, pp. 606–614. doi 10.1111/j.1755-0998.2009.02822.x
Shekhovtsov, S.V., Golovanova, E.V., and Peltek, S.E., Genetic diversity of the earthworm Octolasion tyrtaeum (Lumbricidae, Annelida), Pedobiologia, 2014a, vol. 57, pp. 245–250. doi 10.1016/j.pedobi.2014.09.002
Shekhovtsov, S.V., Golovanova, E.V., and Peltek, S.E., Cryptic diversity within the Nordenskiold’s earthworm, Eisenia nordenskioldi subsp. nordenskioldi (Lumbricidae, Annelida), Eur. J. Soil Biol., 2013, vol. 58, pp. 13–18. doi 10.1016/j.ejsobi.2013.05.004
Shekhovtsov, S.V., Golovanova, E.V., and Peltek, S.E., Invasive lumbricid earthworms of Kamchatka (Oligochaeta), Zool. Stud., 2014b, vol. 53, p. 52. doi 10.1186/s40555-014-0052-0
Shekhovtsov, S.V., Berman, D.I., and Peltek, S.E., Phylogeography of the Earthworm Eisenia nordenskioldi sub sp. nordenskioldi (Lumbricidae, Oligochaeta) in Northeastern Eurasia, Dokl. Biol. Sci., 2015, vol. 461, pp. 1–4. doi 10.1016/j.pedobi.2014.09.002
Striganova, B.R. and Poryadina, N.M., Zhivotnoe naselenie pochv boreal’nykh lesov Zapadno-Sibirskoi ravniny: (The Animal Population of Boreal Forest Soils of the West Siberian Plain), Moscow: KMK, 2005.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S., MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 2011, vol. 28, pp. 2731–2739. doi 10.1093/molbev/msr121
Vsevolodova-Perel’, T.S., Dozhdevye chervi Rossii: Kadastr i opredelitel’: (Earthworms of Russia: The Inventory and Identifier), Moscow: Nauka, 1997.
Waugh, J., DNA barcoding in animal species: Progress, potential and pitfalls, BioEssays, 2007, vol. 29, pp. 188–197. doi 10.1002/bies.20529
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Original Russian Text © S.V. Shekhovtsov, N.E. Bazarova, D.I. Berman, N.A. Bulakhova, E.V. Golovanova, S.V. Konyaev, T.M. Krugova, I.I. Lyubechanskii, S.E. Peltek, 2016, published in Vavilovskii Zhurnal Genetiki i Selektsii, 2016, Vol. 20, No. 1, pp. 125–130.
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Shekhovtsov, S.V., Bazarova, N.E., Berman, D.I. et al. DNA barcoding: How many earthworm species are there in the south of West Siberia?. Russ J Genet Appl Res 7, 57–62 (2017). https://doi.org/10.1134/S2079059717010130
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DOI: https://doi.org/10.1134/S2079059717010130