Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

<p>Abstract</p> <p>Background</p> <p>Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. <it>Calanus sinicus </it>dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies.</p> <p>Results</p> <p>The mitochondrial genome of <it>C. sinicus </it>is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of <it>C. sinicus </it>include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes <it>atp6 </it>and <it>atp8 </it>relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 <it>C. sinicus </it>mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci.</p> <p>Conclusion</p> <p>The occurrence of the <it>circular subgenomic fragment </it>during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of <it>C. sinicus </it>during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of <it>C. sinicus </it>mitogenomes provide a solid foundation for population genetic studies.</p

First record of the freshwater copepod Eucyclops titicacae Kiefer, 1957, new rank (Copepoda, Cyclopoida) in Colombia

The freshwater cyclopoid copepod Eucyclops titicacae Kiefer, 1957, new rank, was previously known as a subspecies of E. neumani (Pesta, 1927). Hitherto, it was recorded only from Lake Titicaca in Peru and Lake Valencia in Venezuela. This species is here recorded from Laguna Nav&#237;o Quebrado, La Guajira, northern Colombia. This is the first record of E. titicacae in Colombia and the third locality in which this species has been reported from. We provide comparative data on the morphology of this copepod. The Colombian specimens have the combination of diagnostic features of E. neumani titicacae as reported in both the original description and subsequent taxonomical accounts, including: 1) spinules on caudal rami not reaching halfway the outer margin; 2) caudal rami length/width ratio= 6.0; 3) length/width ratio of third endopodal segment of fourth leg=1.66; 4) inner spine of fifth leg being shorter than the two adjacent setae. The consistent morphologic differences and the isolation of E. neumani titicacae with respect to E. neumani neumani, each related to a different biogeographic subregion in South America, support the notion that these are two separate species, E. neumani and E. titicacae. Considering this interesting addition, the number of species of Eucyclops known from Colombia increases to 8; a key for the identification of these species is also provided