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Lyubechanskii II, Golovanova EV, Dudko RY, Azarkina GN, Rusalimova OA, Samoylova ES, Shekhovtsov SV, Barsukov PA. Impact of No-Tillage on Soil Invertebrate Communities in the Southern Forest Steppe of West Siberia: Preliminary Research. Diversity 2023; 15:402. [DOI: 10.3390/d15030402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The aim of our study is to assess changes in soil macroinvertebrate biodiversity when conventional tillage (CT) is replaced by no-tillage (NT) in agroecosystems of the southern part of the West Siberian forest steppe. The research was conducted in the Novosibirsk region at the end of May 2017, May 2018, and in June 2018. The agricultural plots with CT and NT were located close to each other on identical soils, at a distance of about 200 m from the nearest forest shelterbelts. NT technology has been applied on the experimental plot since 2007. Sampling of invertebrates was conducted in two ways, namely soil sampling and pitfall trapping. The majority of basic physicochemical properties of soil were the same or similar between the CT and NT plots. However, depending on the type of tillage, different soil invertebrate communities had already developed in the control (CT) and experimental (NT) plots during this time. The community of the CT plot includes a large number of flying predatory Carabidae species typical of early successional stages (such as Bembidion properans and B. quadrimaculatum, Poecilus spp.) and phytophages, i.e., larvae of Elateridae. The NT plot has significantly higher density and species richness of earthworms (Eisenia nordenskioldi and synanthropic E. fetida in the NT plot versus one individual of E. nordenskioldi in the CT plot). The NT plot has a significantly richer and more abundant assemblage of spiders (especially in spring) and a poor assemblage of insect predators (except for the superdominant ground beetle Poecilus cupreus and the subdominant P. versicolor in summer 2018). Large numbers of larvae of some carabids (e.g., Amara consularis) were found in the NT soil, suggesting that they complete a full life cycle in this habitat.
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Shekhovtsov SV, Efremov YR, Poluboyarova TV, Peltek SE. Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2021; 25:647-651. [PMID: 34782884 PMCID: PMC8558923 DOI: 10.18699/vj21.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022] Open
Abstract
The size of the nuclear genome in eukaryotes is mostly determined by mobile elements and noncoding
sequences and may vary within wide limits. It can differ signif icantly both among higher-order taxa and closely
related species within a genus; genome size is known to be uncorrelated with organism complexity (the so-called
C-paradox). Less is known about intraspecif ic variation of this parameter. Typically, genome size is stable within a
species, and the known exceptions turn out be cryptic taxa. The Eisenia nordenskioldi complex encompasses several
closely related earthworm species. They are widely distributed in the Urals, Siberia, and the Russian Far East, as
well as adjacent regions. This complex is characterized by signif icant morphological, chromosomal, ecological, and
genetic variation. The aim of our study was to estimate the nuclear genome size in several genetic lineages of the
E. nordenskioldi complex using f low cytometry. The genome size in different genetic lineages differed strongly,
which supports the hypothesis that they are separate species. We found two groups of lineages, with small
(250–500 Mbp) and large (2300–3500 Mbp) genomes. Moreover, different populations within one lineage also
demonstrated variation in genome size (15–25 %). We compared the obtained data to phylogenetic trees based
on transcriptome data. Genome size in ancestral population was more likely to be big. It increased or decreased
independently in different lineages, and these processes could be associated with changes in genome size and/or
transition to endogeic lifestyle.
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Affiliation(s)
| | - Ya R Efremov
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | | | - S E Peltek
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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Lone AR, Thakur SS, Tiwari N, Olusola B. Sokefun, Yadav S. Disentangling earthworm taxonomic stumbling blocks using molecular markers. J Threat Taxa 2021. [DOI: 10.11609/jott.6888.13.11.19566-19579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Taxonomic classification of earthworms based on anatomical features has created several challenges for systematics and population genetics. This study examines the application of molecular markers, in particular mitochondrial cytochrome oxidase (COI), to facilitate discrimination of closely related earthworm species. Molecular markers have also provided insights into population genetics by aiding assessment of genetic diversity, lineage sorting, and genealogical distributions of populations for several species. Phylogeography—a study that evaluates the geographical distribution of these genealogical lineages and the role of historical processes in shaping their distribution—has also provided insights into ecology and biodiversity. Such studies are also essential to understand the distribution patterns of invasive earthworm species that have been introduced in non-native ecosystems globally. The negative consequences of these invasions on native species include competition for food resources and altered ecosystems. We anticipate that molecular markers such as COI and DNA barcoding offer potential solutions to disentangling taxonomic impediments in earthworms and advancing their systematics and population genetics.
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Shekhovtsov SV, Shipova AA, Poluboyarova TV, Vasiliev GV, Golovanova EV, Geraskina AP, Bulakhova NA, Szederjesi T, Peltek SE. Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data. Front Genet 2020; 11:598196. [PMID: 33365049 PMCID: PMC7750196 DOI: 10.3389/fgene.2020.598196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/09/2020] [Indexed: 01/22/2023] Open
Abstract
Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.
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Affiliation(s)
- Sergei V Shekhovtsov
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Aleksandra A Shipova
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatiana V Poluboyarova
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Gennady V Vasiliev
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Golovanova
- Laboratory of Systematics and Ecology of Invertebrates, Omsk State Pedagogical University, Omsk, Russia
| | - Anna P Geraskina
- Center for Forest Ecology and Productivity of the Russian Academy of Sciences, Moscow, Russia
| | - Nina A Bulakhova
- Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia.,Laboratory of Biodiversity and Ecology, Tomsk State University, Tomsk, Russia
| | - Tímea Szederjesi
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Sergei E Peltek
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Berman DI, Bulakhova NA, Meshcheryakova EN, Shekhovtsov SV. Cold Resistance and the Distribution of Genetic Lineages of the Earthworm Eisenia nordenskioldi (Oligochaeta, Lumbricidae). BIOL BULL+ 2019. [DOI: 10.1134/s1062359019050042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
BACKGROUND Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within Eisenia nordenskioldi nordenskioldi, an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic E. andrei, and Lumbricus rubellus. RESULTS We de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric E. andrei. Both datasets yielded phylogenetic trees with the same topology. E. n. nordenskioldi was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal. CONCLUSIONS We found that genetic lineages of E. n. nordenskioldi are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the E. nordenskioldi species complex.
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Affiliation(s)
- Sergei V. Shekhovtsov
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
- Institute of Biological Problems of the North FEB RAS, Portovaya St. 18, Magadan, 685000 Russia
| | - Nikita I. Ershov
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| | - Sergey E. Peltek
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
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Taheri S, James S, Roy V, Decaëns T, Williams B, Anderson F, Rougerie R, Chang CH, Brown G, Cunha L, Stanton D, Da Silva E, Chen JH, Lemmon A, Moriarty Lemmon E, Bartz M, Baretta D, Barois I, Lapied E, Coulis M, Dupont L. Complex taxonomy of the ‘brush tail’ peregrine earthworm Pontoscolex corethrurus. Mol Phylogenet Evol 2018; 124:60-70. [DOI: 10.1016/j.ympev.2018.02.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 01/19/2023]
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Shekhovtsov SV, Berman DI, Bulakhova NA, Makarova OL, Peltek SE. Phylogeography of earthworms from high latitudes of Eurasia. ACTA ZOOL ACAD SCI H 2018. [DOI: 10.17109/azh.64.4.369.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Shekhovtsov SV, Berman DI, Bulakhova NA, Vinokurov NN, Peltek SE. Phylogeography of Eisenia nordenskioldi nordenskioldi (Lumbricidae, Oligochaeta) from the north of Asia. Polar Biol 2017. [DOI: 10.1007/s00300-017-2184-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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