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Shekhovtsov SV, Derzhinsky YA, Golovanova EV. Earthworm (Oligochaeta, Lumbricidae) intraspecific genetic variation and polyploidy. Vavilovskii Zhurnal Genet Selektsii 2024; 28:563-570. [PMID: 39280850 PMCID: PMC11393649 DOI: 10.18699/vjgb-24-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 09/18/2024] Open
Abstract
Earthworms are known for their intricate systematics and a diverse range of reproduction modes, including outcrossing, self-fertilization, parthenogenesis, and some other modes, which can occasionally coexist in a single species. Moreover, they exhibit considerable intraspecific karyotype diversity, with ploidy levels varying from di- to decaploid, as well as high genetic variation. In some cases, a single species may exhibit significant morphological variation, contain several races of different ploidy, and harbor multiple genetic lineages that display significant divergence in both nuclear and mitochondrial DNA. However, the relationship between ploidy races and genetic lineages in earthworms remains largely unexplored. To address this question, we conducted a comprehensive review of available data on earthworm genetic diversity and karyotypes. Our analysis revealed that in many cases, a single genetic lineage appears to encompass populations with different ploidy levels, indicating recent polyploidization. On the other hand, some other cases like Octolasion tyrtaeum and Dendrobaena schmidti/D. tellermanica demonstrate pronounced genetic boundaries between ploidy races, implying that they diverged long ago. Certain cases like the Eisenia nordenskioldi complex represent a complex picture with ancient divergence between lineages and both ancient and recent polyploidization. The comparison of phylogenetic and cytological data suggests that some ploidy races have arisen independently multiple times, which supports the early findings by T.S. Vsevolodova-Perel and T.V. Malinina. The key to such a complex picture is probably the plasticity of reproductive modes in earthworms, which encompass diverse modes of sexual and asexual reproduction; also, it has been demonstrated that even high-ploidy forms can retain amphimixis.
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Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Ye A Derzhinsky
- Vitebsk State University named after P.M. Masherov, Vitebsk, Belarus
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Chang CH, Shen HP, Sherlock E, Csuzdi C. A review of the earthworm Amynthasmasatakae (Beddard, 1892) (Clitellata, Megascolecidae), with designation of two new synonyms. Biodivers Data J 2024; 12:e119599. [PMID: 38765273 PMCID: PMC11099468 DOI: 10.3897/bdj.12.e119599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/13/2024] [Indexed: 05/21/2024] Open
Abstract
Correct and timely identification of an invasive species during quarantine or at an early stage of invasion before establishment or spread is critical for preventing biological invasions. However, taxonomic confusion of potential invasive earthworm species caused by incorrect taxonomic treatment or reckless taxonomic work has made it difficult to properly recognize potential invasion threats. Through analyzing publicly available DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene, we confirmed the validity of the specific status of Amynthasmasatakae (Beddard, 1892), a peregrine earthworm species in East Asia with the potential to spread to other regions of the world, and designated two new synonyms of A.masatakae: Amynthastralfamadore Blakemore, 2012 syn. nov. and Amynthasscaberulus Sun and Jiang, 2021 syn. nov. Additionally, the name A.triastriatususualis Dong, Jiang, Yuan, Zhao and Qiu, 2020 is nomenclaturally unavailable since it was published in an electronic journal without ZooBank registration and an explicit statement establishing a new nominal taxon. Specimens described under this unavailable name actually belong to A.masatakae. Inadequate literature review and erroneous species identities associated with sequences in GenBank have caused even more problems in the already confusing earthworm taxonomy.
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Affiliation(s)
- Chih-Han Chang
- Department of Life Science and Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, TaiwanDepartment of Life Science and Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipeiTaiwan
| | - Huei-Ping Shen
- Taiwan Biodiversity Research Institute, Ministry of Agriculture, Nantou, TaiwanTaiwan Biodiversity Research Institute, Ministry of AgricultureNantouTaiwan
| | - Emma Sherlock
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| | - Csaba Csuzdi
- Department of Zoology, Eszterházy Károly Catholic University, Eger, HungaryDepartment of Zoology, Eszterházy Károly Catholic UniversityEgerHungary
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Pinadero SJ, Marchán DF, Navarro AM, Tilikj N, Novo M, Domínguez J, Díaz Cosín DJ, Trigo D. Comparative phylogeography and integrative systematic revision of Iberian endemic earthworms (Crassiclitellata, Lumbricidae). ZOOL SCR 2023. [DOI: 10.1111/zsc.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Sergio Jiménez Pinadero
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
| | - Daniel Fernández Marchán
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
| | - Alejandro Martínez Navarro
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
| | - Natasha Tilikj
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
| | - Marta Novo
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
| | - Jorge Domínguez
- Grupo de Ecoloxía Animal (GEA) Universidade de Vigo Vigo Spain
| | - Darío J. Díaz Cosín
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
| | - Dolores Trigo
- Biodiversity, Ecology and Evolution Department, Faculty of Biology Universidad Complutense de Madrid Madrid Spain
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A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Dupont L, Audusseau H, Porco D, Butt KR. Mitonuclear discordance and patterns of reproductive isolation in a complex of simultaneously hermaphroditic species, the Allolobophora chlorotica case study. J Evol Biol 2022; 35:831-843. [PMID: 35567785 PMCID: PMC9322523 DOI: 10.1111/jeb.14017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/04/2022] [Accepted: 04/12/2022] [Indexed: 12/01/2022]
Abstract
Historical events of population fragmentation, expansion and admixture over geological time may result in complex patterns of reproductive isolation and may explain why, for some taxa, the study of mitochondrial (mt) and nuclear (nu) genetic data results in discordant evolutionary patterns. Complex patterns of taxonomic diversity were recently revealed in earthworms for which distribution is largely the result of paleogeographical events. Here, we investigated reproductive isolation patterns in a complex of cryptic species of earthworms in which discordant patterns between mt and nu genetic lineages were previously revealed, the Allolobophora chlorotica aggregate. Using four nu microsatellite markers and a fragment of the cytochrome c oxidase subunit I mt gene, we carried out a parentage analysis to investigate the mating patterns (i) between individuals belonging to two divergent mt lineages that cannot be distinguished with nu markers and (ii) between individuals belonging to lineages that are differentiated both at the mt and nu levels. Amongst the 157 field-collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mt lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In crosses between lineages that diverged exclusively at the mt level, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest concerning the use of male/female function between mating partners. In crosses between lineages that diverged both at the mt and nu levels, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Different degrees of reproductive isolation, from differential sex allocation to post-zygotic isolation, were thus revealed. Lineages appear to be at different stages in the speciation process, which likely explain the observed opposite patterns of mitonuclear congruence.
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Affiliation(s)
- Lise Dupont
- University of Paris-Est Creteil, CNRS, INRAE, IRD, IEES-Paris, Creteil, France.,Sorbonne Université, IEES-Paris, Paris, France.,Université de Paris, IEES-Paris, Paris, France
| | - Hélène Audusseau
- ECOBIO [(Ecosystèmes, Biodiversité, Evolution)]-UMR 6553, University of Rennes, CNRS, Rennes, France
| | - David Porco
- Musée National d'histoire Naturelle, Luxembourg, Luxembourg
| | - Kevin R Butt
- School of Natural Sciences, University of Central Lancashire, Preston, UK
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Potapov A, Schaefer I, Jochum M, Widyastuti R, Eisenhauer N, Scheu S. Oil palm and rubber expansion facilitates earthworm invasion in Indonesia. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02539-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AbstractDeforestation, plantation expansion and other human activities in tropical ecosystems are often associated with biological invasions. These processes have been studied for above-ground organisms, but associated changes below the ground have received little attention. We surveyed rainforest and plantation systems in Jambi province, Sumatra, Indonesia, to investigate effects of land-use change on the diversity and abundance of earthworms—a major group of soil-ecosystem engineers that often is associated with human activities. Density and biomass of earthworms increased 4—30-fold in oil palm and rubber monoculture plantations compared to rainforest. Despite much higher abundance, earthworm communities in plantations were less diverse and dominated by the peregrine morphospecies Pontoscolex corethrurus, often recorded as invasive. Considering the high deforestation rate in Indonesia, invasive earthworms are expected to dominate soil communities across the region in the near future, in lieu of native soil biodiversity. Ecologically-friendly management approaches, increasing structural habitat complexity and plant diversity, may foster beneficial effects of invasive earthworms on plant growth while mitigating negative effects on below-ground biodiversity and the functioning of the native soil animal community.
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Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.
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James SW, Csuzdi C, Chang CH, Aspe NM, Jiménez JJ, Feijoo A, Blouin M, Lavelle P. Comment on "Global distribution of earthworm diversity". Science 2021; 371:371/6525/eabe4629. [PMID: 33414190 DOI: 10.1126/science.abe4629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022]
Abstract
Phillips et al (Reports, 25 October 2019, p. 480) incorrectly conclude that tropical earthworm communities are less diverse and abundant than temperate communities. This result is an artifact generated by some low-quality datasets, lower sampling intensity in the tropics, different patterns in richness-area relationships, the occurrence of invasive species in managed soils, and a focus on local rather than regional richness.
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Affiliation(s)
- S W James
- Sustainable Living Department, Maharishi International University, Fairfield, IA 52557, USA.
| | - C Csuzdi
- Eszterházy Károly University, Eger, Hungary
| | - C-H Chang
- Department of Life Science and Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - N M Aspe
- College of Science and Environment, Mindanao State University at Naawan, 9023 Naawan, Misamis Oriental, Philippines
| | - J J Jiménez
- ARAID, Soil Ecology, IPE-CSIC, Jaca 22700 (Huesca), Spain
| | - A Feijoo
- School of Environmental Sciences, Universidad Tecnológica de Pereira, Complejo la Julita, Pereira AA 097, Colombia
| | - M Blouin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne Franche Comté, F-21000 Dijon, France
| | - P Lavelle
- Université Paris Sorbonne, IEES-Biodis, Paris, France.
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Martinsson S, Klinth M, Erséus C. Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation. BMC Evol Biol 2020; 20:116. [PMID: 32928097 PMCID: PMC7488859 DOI: 10.1186/s12862-020-01678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. RESULTS A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. CONCLUSION We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.
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Affiliation(s)
- Svante Martinsson
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.
| | - Mårten Klinth
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Christer Erséus
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
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Genetic evidence of multiple introductions and mixed reproductive strategy in the peregrine earthworm Pontoscolex corethrurus. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02270-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI. Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. Zookeys 2020; 941:49-69. [PMID: 32595407 PMCID: PMC7311532 DOI: 10.3897/zookeys.941.49319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/13/2020] [Indexed: 11/22/2022] Open
Abstract
Pontoscolexcorethrurus (Müller, 1857) is an invasive tropical earthworm, globally distributed. It reproduces through parthenogenesis, which theoretically results in low genetic diversity. The analysis of the population structure of P.corethrurus using molecular markers may significantly contribute to understanding the ecology and reproductive system of this earthworm species. This work assessed the genetic diversity and population structure of P.corethrurus with 34 polymorphic inter simple sequence repeat markers, covering four populations in tropical and temperate pastures from Veracruz State. Nuclear markers distinguished two genetic clusters, probably corresponding to two distinct genetic lineages. The number of clones detected in the AC population was lower than expected for a parthenogenetic species. Also, the apparent lack of differences in population structures related to the geographic region among the populations studied may indicate that human-mediated transference is prevalent in these areas. Still, most individuals apparently belong to lineage A, and only a few individuals seem to belong to the lineage B. Thus, the admixture signatures found among the four populations of P.corethrurus may have facilitated a successful invasion by directly increasing fitness. In summary, addressing the genetic variation of P.corethrurus with ISSR markers was a suitable approach, as it evidenced the genetic diversity and relationships in the populations evaluated.
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Affiliation(s)
- Diana Ortíz-Gamino
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana. Av. de las Culturas Veracruzanas No. 101, Col. Emiliano Zapata, 91090 Xalapa, Veracruz, México Universidad Veracruzana Xalapa Mexico.,Subdirección de Recursos Naturales y Cambio Climático del H. Ayuntamiento de Xalapa, Calle Volcán de Colima 7, Coapexpan 91070, Xalapa, Veracruz, México Subdirección de Recursos Naturales y Cambio Climático del H. Ayuntamiento de Xalapa Xalapa Mexico
| | - Josefat Gregorio
- Consejo Nacional de Ciencia y Tecnología - Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Del. Benito Juárez, Ciudad de México, 03940, México Instituto Politécnico Nacional Mexico Mexico
| | - Luis Cunha
- School of Applied Sciences, University of South Wales, Pontypridd, UK University of South Wales Pontypridd United Kingdom
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Campus Morelos, Av. Universidad s/n Col. Chamilpa 62210, Cuernavaca, Morelos, México Universidad Nacional Autónoma de México Campus Morelos Cuernavaca Mexico
| | - Carlos Fragoso
- Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, El Haya 91070, Xalapa, Veracruz, México Instituto de Ecología Xalapa Mexico
| | - Ángel I Ortíz-Ceballos
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana. Av. de las Culturas Veracruzanas No. 101, Col. Emiliano Zapata, 91090 Xalapa, Veracruz, México Universidad Veracruzana Xalapa Mexico
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Liu H, Xu N, Zhang Q, Wang G, Xu H, Ruan H. Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora, Moniligastridae) and comparison with other Metagynophora species. Genomics 2020; 112:3056-3064. [PMID: 32454169 DOI: 10.1016/j.ygeno.2020.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/04/2020] [Accepted: 05/20/2020] [Indexed: 02/03/2023]
Abstract
Here, the complete mitochondrial genome (mitogenome) of Drawida gisti was sequenced and compared with the mitogenomes of other Metagynophora species. The circular mitogenome was 14,648 bp in length and contained two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The types of constitutive genes and the direction of the coding strand that appeared in Drawida mitogenome were identical to those observed in other Metagynophora species, except for a missing lengthy non-coding region. The conservative relationships between Drawida species were supported by the overall analyses of 13 PCGs, two rRNAs, and 22 tRNAs. A comparison of the Metagynophora mitogenomes revealed that the ATP8 gene possessed the highest polymorphism among the 13 PCGs and two rRNAs. Phylogenetic analysis suggested that the Moniligastridae contained Drawida, which is a primitive Metagynophora group. Our study provides a step forward toward elucidating the evolutionary linkages within Drawida and even Metagynophora.
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Affiliation(s)
- Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Qingzheng Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Guobing Wang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hanmei Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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Marchán DF, Fernández R, Domínguez J, Díaz Cosín DJ, Novo M. Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Daniel Fernández Marchán
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC-Universitat, Pompeu Fabra), Passeig Marítim de la Barceloneta 37-,49, Barcelona, 08003, Spain
| | - Jorge Domínguez
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain
| | - Darío J. Díaz Cosín
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Novo
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
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Local adaptation fuels cryptic speciation in terrestrial annelids. Mol Phylogenet Evol 2020; 146:106767. [PMID: 32081763 DOI: 10.1016/j.ympev.2020.106767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/13/2020] [Indexed: 11/23/2022]
Abstract
Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as it is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between 17 populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.
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Ortíz-Ceballos AI, Ortiz-Gamino D, Andrade-Torres A, Pérez-Rodríguez P, López-Ortega M. Pontoscolex corethrurus: A homeless invasive tropical earthworm? PLoS One 2019; 14:e0222337. [PMID: 31539381 PMCID: PMC6754163 DOI: 10.1371/journal.pone.0222337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 11/18/2022] Open
Abstract
The presence of earthworm species in crop fields is as old as agriculture itself. The earthworms Pontoscolex corethrurus (invasive) and Balanteodrilus pearsei (native) are associated with the emergence of agriculture and sedentism in the region Amazon and Maya, respectively. Both species have shifted their preference from their natural habitat to the cropland niche. They contrast in terms of intensification of agricultural land use (anthropic impact to the symbiotic soil microbiome). P. corethrurus inhabits conventional agroecosystems, while B. pearsei thrives in traditional agroecosystems, i.e., P. corethrurus has not yet been recorded in soils where B. pearsei dwells. The demographic behavior of these two earthworm species was assessed in the laboratory over 100 days, according to their origin (OE; P. corethrurus and B. pearsei) food quality (FQ; soil only, maize stubble, Mucuna pruriens), and soil moisture (SM; 25, 33, 42%). The results showed that OE, FQ, SM, and the OE x FQ interaction were highly significant for the survival, growth, and reproduction of earthworms. P. corethrurus showed a lower survival rate (> mortality). P. corethrurus survivors fed a diet of low-to-intermediate nutritional quality (soil and stubble maize, respectively) showed a greater capacity to grow and reproduce; however, it was surpassed by the native earthworm when fed a high-quality diet (M. pruriens). Besides, P. corethrurus displayed a low cocoon hatching (emergence of juveniles). These results suggest that the presence of the invasive species was associated with a negative interaction with the soil microbiota where the native species dwells, and with the absence of natural mutualistic bacteria (gut, nephridia, and cocoons). These results are consistent with the absence of P. corethrurus in milpa and pasture-type agricultural niches managed by peasants (agroecologists) to grow food regularly through biological soil management. Results reported here suggest that P. corethrurus is an invasive species that is neither wild nor domesticated, that is, its eco-evolutionary phylogeny needs to be derived based on its symbionts.
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Affiliation(s)
- Angel I. Ortíz-Ceballos
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Col. Emiliano Zapata, Xalapa, Veracruz, México
- * E-mail:
| | - Diana Ortiz-Gamino
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Col. Emiliano Zapata, Xalapa, Veracruz, México
| | - Antonio Andrade-Torres
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Col. Emiliano Zapata, Xalapa, Veracruz, México
| | - Paulino Pérez-Rodríguez
- Programa de Estadística, Campus Montecillo, Colegio de Postgraduados, Montecillo, Estado de México, México
| | - Maurilio López-Ortega
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Col. Emiliano Zapata, Xalapa, Veracruz, México
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16
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Jirapatrasilp P, Backeljau T, Prasankok P, Chanabun R, Panha S. Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus). Mol Phylogenet Evol 2019; 139:106531. [PMID: 31185298 DOI: 10.1016/j.ympev.2019.106531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/19/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022]
Abstract
Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.
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Affiliation(s)
- Parin Jirapatrasilp
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Pongpun Prasankok
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agriculture Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon 47000, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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17
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Erséus C, Klinth MJ, Rota E, De Wit P, Gustafsson DR, Martinsson S. The popular model annelid Enchytraeus albidus is only one species in a complex of seashore white worms (Clitellata, Enchytraeidae). ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00402-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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