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Diversity
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Molecular Phylogeny and Evolution of Earthworms
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Molecular Phylogeny and Evolution of Earthworms

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 17589

Special Issue Editor

Dr. Daniel Fernández Marchán

E-Mail Website
Guest Editor
Centre d’Ecologie Fonctionelle et Evolutive UMR 5175 CNRS, Montpellier, France
Interests: PCR; DNA sequencing; evolution; biodiversity; ecology and evolution; conservation biology; genetics; ecology; earthworms; species diversity

Special Issue Information

Dear Colleagues,

Earthworms (Annelida, Crassiclitellata) are an ancient (more than 200 Mya old—Erséus et al. 2019), highly diverse (more than 6000 species in 18 families—Anderson et al. 2017), and widely distributed group that usually constitute the dominant element of soil communities. Despite their ecological relevance, there remains a strong taxonomic deficit related to the inaccessibility of their habitat. In addition, their morphology is challenging to taxonomize due to pervasive convergence and homoplasy, usually confounding phylogenetic relationships and hiding cryptic diversity. Thus, the advent of molecular phylogenetic techniques has allowed us to surpass these limitations, shedding light on the origin, diversification, and evolutionary relationships of earthworm taxa. Yet, the application of these techniques to the topic is far from being widespread, while countless questions stand unanswered. These involve all the different taxonomic levels: where and when did the different families originate and diversify? Why are different earthworm genera so much more diverse than others? What variables explain the contrasting phylogeographic patterns observed in different earthworm species?—and that’s just a start.

This Special Issue seeks to bring together significant contributions to our understanding of the evolution of earthworms, stemming from the application of the diverse range of molecular phylogenetic techniques (barcoding, multilocus phylogenetics, NGS) to the whole spectrum of earthworm diversity. We invite you to submit a paper including any of these topics, from a molecular-phylogenetics-guided alpha taxonomy to integrative systematic revisions, phylogeography, or comparative phylogenetic methods across different families. Please do not hesitate to contact the editorial team if you have any questions.

Dr. Daniel Fernández Marchán
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • earthworms
  • evolution
  • molecular phylogenetics
  • integrative taxonomy
  • barcoding
  • phylogenomics
  • multilocus phylogenies
  • phylogeography
  • historical biogeography

Published Papers (7 papers)

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25 pages, 7668 KiB  
Article
Phylogenetic Relationships in Earthworm Megascolex Species (Oligochaeta: Megascolecidae) with Addition of Two New Species
by Azhar Rashid Lone, Samrendra Singh Thakur, Pooja Tiwari, Samuel Wooster James and Shweta Yadav
Diversity 2022, 14(11), 1006; https://doi.org/10.3390/d14111006 - 20 Nov 2022
Cited by 3 | Viewed by 2082
Abstract
Megascolex (Oligochaeta: Megascolecidae) are endemic species to India and Sri Lanka, however, to date their molecular taxonomy and phylogenetic relationships have not been reported. We applied the first integrative approach using morpho-anatomical features and a COI dataset to unveil species delimitation (SD), molecular [...] Read more.
Megascolex (Oligochaeta: Megascolecidae) are endemic species to India and Sri Lanka, however, to date their molecular taxonomy and phylogenetic relationships have not been reported. We applied the first integrative approach using morpho-anatomical features and a COI dataset to unveil species delimitation (SD), molecular taxonomy, and phylogenetic relationships in Megascolex species. Our morpho-anatomical results revealed nine Megascolex species, namely, M. auriculata, M. cochinensis cochinensis, M. filiciseta, M. ratus, M. travancorensis travancorensis, M. triangularis, M. konkanensis konkanensis, M. polytheca polytheca, and M. polytheca zonatus. We also reported the occurrence of two new species, namely, M. papparensis sp. nov, and M. vazhichlensis sp. nov. Such findings were also supported by the analysed COI dataset, in which these new species appeared distinct on the phylogenetic trees with strong support. The studied Megascolex species appeared paraphyletic and formed three subclades on Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic trees. The first clade consisted of six species: M. cochinensis cochinensis, M. polytheca polytheca, M. polytheca zonatus, M. konkanensis konkanensis, M. filiciseta, and M. auriculata with strong posterior probability support. The second clade consisted of M. travancorensis travancorensis, M. papparensis sp. nov, and M. vazhichlensis sp. nov with strong support. The third clade consisted of M. ratus and M. triangularis with good support. In addition, the validation of species was confirmed by SD methods, in which the congruence among OTUs was observed with the clear barcode gap of 12–14% suggested by ABGD analysis. However, the species M. ratus and M. travancorensis travancorensis show deep intraspecific divergence and, therefore, require more sampling data. Such findings are essential to study the phylogenetics and evolution of the genus and, nonetheless, demand larger COI datasets to make concrete conclusions. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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16 pages, 4375 KiB  
Article
OTU Delimitation with Earthworm DNA Barcodes: A Comparison of Methods
by Arnaud Goulpeau, Benoit Penel, Marie-Eugénie Maggia, Daniel Fernández Marchán, Dirk Steinke, Mickaël Hedde and Thibaud Decaëns
Diversity 2022, 14(10), 866; https://doi.org/10.3390/d14100866 - 13 Oct 2022
Cited by 8 | Viewed by 2003
Abstract
Although DNA barcodes-based operational taxonomic units (OTUs) are increasingly used in earthworm research, the relative efficiency of the different methods available to delimit them has not yet been tested on a comprehensive dataset. For this study, we used three datasets containing 651, 2304 [...] Read more.
Although DNA barcodes-based operational taxonomic units (OTUs) are increasingly used in earthworm research, the relative efficiency of the different methods available to delimit them has not yet been tested on a comprehensive dataset. For this study, we used three datasets containing 651, 2304 and 4773 COI barcodes of earthworms from French Guiana, respectively, to compare five of these methods: two phylogenetic methods—namely Poisson Tree Processes (PTP) and General Mixed Yule Coalescence (GMYC)—and three distance matrix methods—namely Refined Single Linkage (RESL, used for assigning Barcode Index Numbers in the Barcode of Life Data systems), Automatic Barcode Gap Discovery (ABGD), and Assemble Species by Automatic Partitioning (ASAP). We found that phylogenetic approaches are less suitable for delineating OTUs from DNA barcodes in earthworms, especially for large sets of sequences. The computation times are unreasonable, they often fail to converge, and they also show a strong tendency to oversplit species. Among distance-based methods, RESL also has a clear tendency to oversplitting, while ABGD and ASAP are less prone to mismatches and have short computation times. ASAP requires less a priori knowledge for model parameterisation than AGBD, provides efficient graphical outputs, and has a much lower tendency to generate mismatches. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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15 pages, 3253 KiB  
Article
Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae)
by Huifeng Zhao, Shuanghu Fan, Nonillon M. Aspe, Lichao Feng and Yufeng Zhang
Diversity 2022, 14(9), 714; https://doi.org/10.3390/d14090714 - 28 Aug 2022
Cited by 5 | Viewed by 1851
Abstract
Earthworms are an important ecological group, especially in agricultural regions in Northeast China. However, fewer studies focus on this group of organisms compared with other faunal groups. Here, we sequenced 15 new mitogenomes of Aporrectodea tuberculata Eisen, 1874, A. trapezoides Duges, 1828, Eisenia [...] Read more.
Earthworms are an important ecological group, especially in agricultural regions in Northeast China. However, fewer studies focus on this group of organisms compared with other faunal groups. Here, we sequenced 15 new mitogenomes of Aporrectodea tuberculata Eisen, 1874, A. trapezoides Duges, 1828, Eisenia nordenskioldi Eisen, 1878 and Drawida ghilarovi Gates, 1969 in Northeast China using a high-throughput sequencing platform. These incomplete linear and double-stranded mitogenomes vary from 14,998 bp to 16,123 bp in size and include 37 genes and a putative control region. Intraspecific genetic divergence was quantified in the lumbricid species, and a control region in D. ghilarovi was reported for the first time by comparison to the mitogenomes of the congeners. Phylogenetic analysis based on coding genes and ribosomal DNA datasets using BI and ML inferences showed the non-monophyly of Aporrectodea and polyphyly of E. nordenskioldi. Future works should examine the taxonomy, phylogeny and population genetics not only of Lumbricidae but also the other earthworm families on the global scale using mitogenomic and nuclear data. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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20 pages, 4185 KiB  
Article
Population Genetic Structure and Diversity of Metaphire remanens (Oligochaeta: Megascolecidae) Based on Mitochondrial DNA Analysis, with a Note on a New Species of Metaphire remanens sp. nov.
by Qing Jin, Jibao Jiang, Jiali Li and Jiangping Qiu
Diversity 2022, 14(4), 275; https://doi.org/10.3390/d14040275 - 06 Apr 2022
Viewed by 1979
Abstract
Metaphire remanens sp. nov. is widely distributed throughout Hunan Province, China. We sequenced the mitochondrial DNA to investigate its population genetic structure and genetic diversity, including cytochrome c oxidase subunit I, cytochrome c oxidase subunit II, 12S ribosomal (r)RNA, 16S rRNA, and nicotinamide [...] Read more.
Metaphire remanens sp. nov. is widely distributed throughout Hunan Province, China. We sequenced the mitochondrial DNA to investigate its population genetic structure and genetic diversity, including cytochrome c oxidase subunit I, cytochrome c oxidase subunit II, 12S ribosomal (r)RNA, 16S rRNA, and nicotinamide adenine dinucleotide dehydrogenase subunit 1, derived from 39 individuals from seven geographic locations in Hunan Province. The genetic diversity indices showed that populations of M. remanens have a strong genetic structure and obvious dispersal histories. M. remanens did not experience population expansion, except in Xiangtan City. This may be because of its evolution toward parthenogenesis. The divergence time estimates indicated that M. remanens originated at 19.2055 Ma and then generated two main lineages at 1.7334 Ma (Quaternary glaciation). These results indicate that glaciation, geographic isolation, and dispersal ability are significant factors that influence the differentiation and dispersal of M. remanens. In this study, we describe Metaphire remanens sp. nov. in morphology. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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10 pages, 1534 KiB  
Article
Patterns of Genetic Variation in the Eisenia nordenskioldi Complex (Oligochaeta: Lumbricidae) along an Elevation Gradient in Northern China
by Yufeng Zhang, Yiming Zhang, Hui Wu, Congsheng Li, Nonillon M. Aspe and Donghui Wu
Diversity 2022, 14(1), 35; https://doi.org/10.3390/d14010035 - 07 Jan 2022
Cited by 3 | Viewed by 2013
Abstract
Eisenia nordenskioldi is the dominant earthworm species in many tundra and boreal habitats. Nothing is known about the genetic diversity of this species along the elevation gradient in China. This study sampled 28 individuals in the E. nordenskioldi complex from Wuling Mountain, [...] Read more.
Eisenia nordenskioldi is the dominant earthworm species in many tundra and boreal habitats. Nothing is known about the genetic diversity of this species along the elevation gradient in China. This study sampled 28 individuals in the E. nordenskioldi complex from Wuling Mountain, northern China, to examine their external morphology and genetic diversity. Mt. Wuling is the southern limit of the distribution of the E. nordenskioldi complex. The specimens from Mt. Wuling were classified into three groups along an elevation gradient. Mismatch distribution analysis suggested that the Pleistocene glaciations possibly did not significantly affect the distribution of earthworm species in this region. We also found that elevation affected the genetic diversity, but not the external morphology of E. nordenskioldi. Given the altitudinal genetic diversity within the E. nordenskioldi complex, the phylogeography of this species provides important information for the zoogeographic reconstruction of the mountains in northern China. With the relatively limited sample size, the result is not conclusive, and further studies need to be conducted in the future to verify the results. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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8 pages, 1510 KiB  
Article
Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae
by Hongyi Liu, Yufeng Zhang, Wei Xu, Yu Fang and Honghua Ruan
Diversity 2021, 13(11), 580; https://doi.org/10.3390/d13110580 - 14 Nov 2021
Cited by 6 | Viewed by 2150
Abstract
Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus [...] Read more.
Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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13 pages, 1999 KiB  
Perspective
Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions
by Daniel Fernández Marchán, Thibaud Decaëns, Jorge Domínguez and Marta Novo
Diversity 2022, 14(1), 30; https://doi.org/10.3390/d14010030 - 04 Jan 2022
Cited by 6 | Viewed by 3353
Abstract
Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on [...] Read more.
Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation. Full article
(This article belongs to the Special Issue Molecular Phylogeny and Evolution of Earthworms)
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