9th International Symposium on Earthworm EcologyA critique of earthworm molecular phylogenetics
Introduction
Excluding a few aquatic taxa (e.g., Almidae and Eiseniella tetraedra in freshwater habitats and Pontodrilus litoralis in marine littoral sediments), earthworms are terrestrial oligochaetes (Annelida: Clitellata) composed of about 5500 species (Blakemore et al. 2007). These clitellates, sometimes referred to as Crassiclitellata, a group of oligochaetes with multilayered cells on their clitellum, are considered by most researchers a natural group (Erseus 2005). Relationships among families have been debated extensively over the last 120 years, and the contents of suprafamilial taxa have been unstable (Michaelsen, 1900, Gates, 1972, Sims, 1980, Omodeo, 2000). Different authors recognize different numbers of families: 15 by Jamieson (1988), 18 by Blakemore, 2000, Blakemore, 2006 and 21 by Reynolds and Cook (1993). Even in the heavily investigated Lumbricidae, the numbers of genera vary between 6 and 20 genera in the traditional systems by Pop, Zicsi, and Omodeo (summarized in Csuzdi and Zicsi 2003) to 42 (Blakemore 2004) or 45 (Qiu and Bouché 1998).
Molecular phylogenetic analyses have been widely used to test taxonomic, phylogenetic and biogeographic hypotheses since the early 1990s and a total of 19 papers about clitellate phylogeny or systematics were published between 1996 and 2002 (see Erseus 2005 for review). The first molecular phylogenetic study that included earthworms was a study focusing on leeches and their relatives (Siddall et al. 2001), in which a sister group relationship between earthworms and the Enchytraeidae was weakly supported with limited sampling. This relationship was formally hypothesized by Erseus and Kallersjo (2004) using 18S rRNA gene sequences and later in a review of the phylogeny of oligochaetous Clitellata (Erseus 2005). Nevertheless, not until 2002 did the first phylogenetic study focusing on earthworms (Jamieson et al. 2002) get published. In that paper the hypothesis of the clade Crassiclitellata (Jamieson 1988) and the monophyly of the Megascolecidae were supported by 28S, 12S and 16S rRNAs data. Since then, a total of 29 papers have been published in peer-reviewed journals (Table 1). However, most of the papers focused on intraspecific genetic variations, DNA barcoding, and species complexes/groups; only five of the 29 papers focused on interfamilial or intergeneric systematics (Jamieson et al., 2002, Pop et al., 2003, Pop et al., 2007, Buckley et al., 2011, Novo et al., 2011). In addition, of nine papers on earthworm molecular phylogenetics published in the proceedings of the 1st–4th International Oligochaete Taxonomy Meetings, only six dealt with interfamilial or intergeneric systematics (Table 2). Regardless of all the above efforts and the seemingly promising idea that molecular phylogenetics could solve the long-lasting debates on the systematics of earthworms mentioned above, no higher level systematics has been proposed.
The objective of the present study is to review published studies to reveal the evolutionary history and sequence characteristics that present difficulties in earthworm molecular phylogeny. We further discuss the recent progress in different disciplines within earthworm molecular phylogenetics, and highlight challenges and promise.
Section snippets
Multiple levels of rapid divergence
One of the most daunting challenges of earthworm molecular phylogenetics is that it is usually hard to achieve reasonable phylogenetic resolution. In fact, it is a challenge not only for earthworms, but also for the whole Annelida. Martin et al. (2000) argued that the poor resolution of higher level phylogenetic relationships among Clitellata was due to rapid divergence, or radiation at the root of Clitellata phylogeny. McHugh, 2000, McHugh, 2001 proposed the same reason to explain the poorly
Sequence divergences and choice of genes
Different genes evolve at different rates and therefore are suitable for studying different taxonomic levels. At the same time, the same gene may evolve at different rates in different animal taxa. Therefore, for studying earthworm phylogeny, it is important to understand the sequence divergences both among different genes within a taxon and within the same gene across different taxonomic levels.
Here we present a comparison of interspecific sequence divergences within a species group/complex,
Interfamilial and intergeneric systematics
Molecular phylogenetic studies focusing on the whole Crassiclitellata support the monophyly of the Megascolecidae (Jamieson et al. 2002), Ocnerodrilidae, Eudrilidae, Lumbricidae, and Glossoscolecidae (Pop et al. 2005a), but the support for all the above families except the Megascolecidae is weak due to insufficient and biased taxon sampling. Furthermore, many families were not included in the two studies and the interfamilial relationships remained unresolved. Similarly, although some studies
Speciation, molecular clock, and biogeography
Compared to higher level systematics, the studies regarding closely related species have been more fruitful. The systematics of the M. formosae species group of the Megascolecidae and the A. caliginosa species complex of the Lumbricidae were revised or re-evaluated (Chang et al., 2008, Pérez-Losada et al., 2009), and cryptic speciation within Hormogaster elisae s. l. of the Hormogastridae was discovered (Novo et al., 2009, Novo et al., 2010). Among these studies, two different modes of
DNA barcoding and integrative taxonomy
Many genes have been used in earthworms to evaluate cryptic diversity and to help species identification, including 16S rRNA (Boyer and Wratten, 2010) and COII (Heethoff et al. 2004). A 658-bp fragment of the mitochondrial gene COI has been proposed as the standard DNA barcode for most animal taxa (Hebert et al., 2003a, Hebert et al., 2003b), and it has been widely used in earthworms (Chang and Chen, 2005, Pérez-Losada et al., 2005, Chang et al., 2007, Chang et al., 2008, Chang et al., 2009,
Pitfalls and promise
Molecular phylogenetics is now at the point of revolutionizing earthworm systematics. The semi-standardized procedure of data management and sharing through GenBank and the Barcode of Life Data Systems (BOLD, http://www.boldsystems.org/) provides enormous resources for studies that need a large body of data from broad taxonomic and/or geographic sampling. With a large quantity of data, however, good taxonomy is required to ensure quality. In GenBank many specific names that refer to earthworm
Acknowledgements
C.-H. Chang is grateful to Katalin Szlavecz for supporting this work and Jiun-Hong Chen for supporting Chang's earlier work. We are also thankful for the helpful comments made by Carlos Fragoso, Stefan Scheu, and two anonymous reviewers on an earlier version of this manuscript. This study was partially funded by the United States National Science Foundation awards EAR-0748442 and DEB-0516439, the Canadian Centre for DNA Barcoding, and a Marie Curie France Regions fellowship award to the
References (76)
- et al.
Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system
Soil Biol. Biochem.
(2006) - et al.
Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity
Mol. Phylogenet. Evol.
(2011) - et al.
Taxonomic status and intraspecific phylogeography of two sibling species of Metaphire (Oligochaeta: Megascolecidae) in Taiwan
Pedobiologia
(2005) - et al.
Taxonomic re-evaluation of the Taiwanese montane earthworm Amynthas wulinensis Tsai, Shen and Tsai, 2001 (Oligochaeta: Megascolecidae): Polytypic species or species complex?
Org. Divers. Evol.
(2007) - et al.
Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellatam, Megascolecidae)
Mol. Phylogenet. Evol.
(2008) - et al.
Identifying earthworms through DNA barcodes: Pitfalls and promise
Pedobiologia
(2009) - et al.
New insight into the genetic structure of the Allolobophora chlorotica aggregate in Europe using microsatellite and mitochondrial data
Pedobiologia
(2011) - et al.
Phylogenetic analysis of Tubificidae (Annelida, Clitellata) based on 18S rDNA sequences
Mol. Phylogenet. Evol.
(2000) - et al.
A vagrant clone in a peregrine species: Phylogeography, high clonal diversity and geographical distribution in the earthworm Aporrectodea trapezoides (Dugès, 1828)
Soil Biol. Biochem.
(2011) - et al.
Mitochondrial COII sequences indicate that the parthenogenetic earthworm Octolasion tyrtaeum (Savigny 1826) constitutes of two lineages differing in body size and genotype
Pedobiologia
(2004)
Identifying earthworms through DNA barcodes
Pedobiologia
Rapid evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida)
Mol. Phylogenet. Evol.
A phylogeographic study of the Japanese earthworm, Metaphire sieboldi (Horst, 1883) (Oligochaeta: Megascolecidae): Inferences from mitochondrial DNA sequences
Eur. J. Soil Biol.
Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data
Mol. Phylogenet. Evol.
Understanding the biogeography of a group of earthworms in the Mediterranean Basin – the phylogenetic puzzle of Hormogastridae (Clitellata: Oligochaeta)
Mol. Phylogenet. Evol.
Phylogenetic species delimitation of the earthworms Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché, 1972 (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA sequences
Pedobiologia
Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta: Lumbricidae) based on mitochondrial and nuclear DNA sequences
Mol. Phylogenet. Evol.
Use of 18S, 16S rDNA and cytochrome c oxidase sequences in earthworm taxonomy (Oligochaeta, Lumbricidae)
Pedobiologia
Application of 16S, 18S rDNA and COI sequences in the molecular systematics of the earthworm family Lumbricidae (Annelida, Oligochaeta)
Eur. J. Soil Biol.
Validating Livanow: molecular data agree that leeches, branchiobdellidans and Acanthobdella peledina are a monophyletic group of oligochaetes
Mol. Phylogenet. Evol.
Tasmanian Earthworms, Monograph with Review of World Families
A provision list of valid names of Lumbricoidea (Oligochaeta) after Easton, 1983
A series of searchable texts on earthworm biodiversity, ecology and systematics from various regions of the world
Unravelling some Kinki earthworms (Annelida: Oligochaeta: Megadrili: Moniligastridae). Part II
Opusc. Zool. Budapest
Unravelling some Kinki worms (Annelida: Oligochaeta: Megadrili: Moniligastridae). Part I
Opusc. Zool. Budapest
Alien earthworms in the Asia/Pacific region with a checklist of species and the first records of Eukerria saltensis (Oligochaeta: Ocnerodrilidae) and Eiseniella tetraedra (Lumbricidae) from Japan, and Pontoscolex corethrurus (Glossoscolecidae) from Okinawa
Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to the ‘Can of Worms’ theory of cryptic species
ZooKeys
Using molecular tool to identify New Zealand endemic earthworms in a mine restoration project (Oligochaeta: Acanthodrilidae, Lumbricidae, Megascolecidae)
Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?
Soil Biol. Biochem.
Genetic structure of invasive earthworms Dendrobaena octaedra in the boreal forest of Alberta: insights into introduction mechanisms
Mol. Ecol.
Remarks on the molecular phylogeny of the genus Dendrobaena (sensus Pop 1941) based on the investigation of 18S rDNA sequences
NADH dehydrogenase subunit 1 gene of the earthworm Amynthas gracilis (Kinberg, 1867) (Oligochaeta: Megascolecidae), with the discussion on inferring the megascolecid phylogeny using DNA sequences
Taiwania
Earthworms of Hungary (Annelida: Oligochaeta, Lumbricidae)
Revision of the Dendrobaena alpine (Rosa, 1884) species group (Oligochaeta, Lumbricidae) by morphological and molecular methods
Towards integrative taxonomy
Biol. J. Linnean Soc.
Phylogeny of oligochaetous Clitellata
Hydrobiologia
18S rDNA phylogeny of Clitellata (Annelida)
Zool. Scr.
Ultrastructural and molecular insights into three populations of Aporrectodea trapezoides (Dugès, 1828) (Oligochaeta, Lumbricidae) with different reproductive modes
Pedobiologia
Cited by (76)
Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance
2023, Science of the Total EnvironmentOrigin and diversification of pheretimoid megascolecid earthworms in the Japanese Archipelago as revealed by mitogenomic phylogenetics
2023, Molecular Phylogenetics and EvolutionInterrogation of earthworm (Clitellata: Haplotaxida) taxonomy and the DNA sequence database
2021, Journal of Asia-Pacific BiodiversityUntangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus)
2019, Molecular Phylogenetics and Evolution
- 1
Current address: Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA.