Abstract
BackgroundMany 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.ResultsWe 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.ConclusionsWe 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.
Highlights
Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date
Only 1085 out of ~ 10,000 ProteinOrtho orthogroups were present in all sequenced samples
We found that majority of E. andrei transcripts had either one or zero orthologs in transcriptomes of different E. n. nordenskioldi lineages, as well as L. rubellus (Fig. 2)
Summary
Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. In the last decade molecular studies revealed that many earthworm species contain two to five cryptic mitochondrial lineages, with about 10–20% of nucleotide substitutions among them (e.g., [2,3,4,5]). Different lineages are often found in individuals living in sympatry and forming a morphologically uniform sample. It is not yet clear what these genetic lineages are. The other is that this diversity is the result of yet unknown mitochondrial phenomena that are accompanied by no significant differences in nuclear genomes. In some cases genetic isolation exists but is not complete [10]
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