Genetic diversity of populations of the earthworm Lumbricus rubellus (Hoffm.) (Oligochaeta, Lumbricidae)

Shepeleva, O. A.; Kodolova, O. P.; Zhukovskaya, E. A.; Striganova, Bella R.

doi:10.1134/s1062359008020118

Cited by 7 publications

(7 citation statements)

References 8 publications

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“…The ETW dataset is likely quite polymorphic; high levels of polymorphism have been shown in the Lumbricus genus (Kautenburger ; Shepeleva et al . ; Donnelly et al . ).…”

Section: Discussionmentioning

confidence: 99%

“…The three datasets examined here required different values for M. The ETW dataset is likely quite polymorphic; high levels of polymorphism have been shown in the Lumbricus genus (Kautenburger 2006;Shepeleva et al 2008;Donnelly et al 2014). However, the low coverage and potential error in the dataset means a definitive determination of true polymorphism could not be reliably assessed, but M3 provided the highest amount of r80 loci.…”

Section: Discussionmentioning

confidence: 99%

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Lost in parameter space: a road map for stacks

2017

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Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method for genotyping populations of model and non‐model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. Using three empirical RAD‐seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. Visualisation of the metrics plotted for the three RAD‐seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating alignment positions is more effective than aligning raw reads directly to a reference genome. Our methods will help the community in honing the analytical skills necessary to accurately assemble a RAD‐seq dataset.

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“…The ETW dataset is likely quite polymorphic; high levels of polymorphism have been shown in the Lumbricus genus (Kautenburger ; Shepeleva et al . ; Donnelly et al . ).…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Lost in parameter space: a road map for stacks

2017

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“…Morgan, et al (2007) also noted that the genetic background of a population can confound biomarker assays, a further indication that the balance between the sensitive and detoxified metal pools can be altered by microevolutionary events. Given that comprehensive phylogenetic studies on earthworms 5 using mitochondrial and nuclear markers have recently revealed high intra-species genetic diversity (Velavan, et al, 2007;Novo, et al, 2008) and deeply divergent genetic lineages, possibly in some cases corresponding with cryptic species (King, et al, 2008;Shepeleva, et al, 2008;Pérez-Losada, et al, 2009), it is a major omission that, to the best of our knowledge, no studies hitherto have explicitly attempted to describe the cellular partitioning of metals in field populations of earthworms with respect to exposure history and genotype. A recent report (Langdon, et al, 2009) that populations of the species Lumbricus rubellus inhabiting abandoned arsenic mine sites have evolved resistance to the metalloid brings the omission into sharp focus.…”

Section: Introductionmentioning

confidence: 99%

Metal bioaccumulation and cellular fractionation in an epigeic earthworm (Lumbricus rubellus): The interactive influences of population exposure histories, site-specific geochemistry and mitochondrial genotype

André

Stürzenbaum

Kille

et al. 2010

Soil Biology and Biochemistry

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“…It has now been introduced into other regions worldwide, such as North America, Australia, and New Zealand (Shepeleva et al. 2008 ). Like other earthworms, L. rubellus is ecologically and environmentally important.…”

mentioning

confidence: 99%

The complete mitochondrial genome of Lumbricus rubellus (Oligochaeta, Lumbricidae) and its phylogenetic analysis

Zhang

Liu

Zhang

et al. 2019

Mitochondrial DNA Part B

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The complete mitochondrial genome of Lumbricus rubellus was analyzed by next-generation sequencing. The mitogenome was 15,464 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and a non-coding region. The phylogenetic analysis of 13 PCGs within the class Oligochaeta suggested that L. rubellus was placed as sister to L. terrestris of the same genus. The results obtained here can contribute to the phylogenetic analysis of earthworms.

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Genetic diversity of populations of the earthworm Lumbricus rubellus (Hoffm.) (Oligochaeta, Lumbricidae)

Cited by 7 publications

References 8 publications

Lost in parameter space: a road map for stacks

Lost in parameter space: a road map for stacks

Metal bioaccumulation and cellular fractionation in an epigeic earthworm (Lumbricus rubellus): The interactive influences of population exposure histories, site-specific geochemistry and mitochondrial genotype

The complete mitochondrial genome of Lumbricus rubellus (Oligochaeta, Lumbricidae) and its phylogenetic analysis

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