Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus <i>Stygobromus</i> (Crustacea: Amphipoda)

Zou

et al. 2020

Preprint

Inversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements.We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.

Section: Peracarida)mentioning

confidence: 99%

Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes

Zou

et al. 2020

Preprint

Mitochondrial DNA Part B

“…Eastern China, Korean Peninsula, Japan, and Russian Far East (Sidorov and Holsinger 2007;Tomikawa et al 2016;Zhao and Hou 2017). Previous studies focusing on stygobitic amphipod species distributed in Europe and North America shed light onto the variability of the mitogenome gene order in Amphipoda (Bauz a- Ribot et al 2009;Aunins et al 2016). Accordingly, it is feasible that mitogenome information of the Asian Pseudocrangonyx species will lead us a further understanding of the evolutionary history of the gene arrangement of this peracaridan group.…”

mentioning

confidence: 99%

The complete mitochondrial genome of Pseudocrangonyx daejeonensis (Crustacea: Amphipoda: Pseudocrangonyctidae)

Lee

Nakano

Tomikawa

et al. 2018

The complete mitogenome sequence of a subterranean pseudocrangonyctid amphipod, Pseudocrangonyx daejeonensis, was determined. The complete mitogenome of P. daejeonensis was 15,069 bp in length with the typical 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). This is the first complete mitogenome sequence in the family Pseudocrangonyctidae. Interestingly, gene arrangements of most amphipod species were almost identical to the typical pan-crustacean ground pattern, whereas two PCGs, both of rRNAs and CR were translocated in P. daejeonensis. A maximum-likelihood tree, constructed based on 30 eumalacostracan mitogenomes, confirmed that P. daejeonensis is closely related to the crangonyctid Stygobromus indentatus and S. tenuis potomacus and supported the monophyly of the superfamily Crangonyctoidea.

“…The gene content generally is highly conserved, with 37 genes encoding for 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one control region (CR) containing regulatory elements for transcription and replication. In amphipods, mitogenomic features such as alterations in gene order, strand bias reversion, presence of additional tRNA genes and CR duplication have been reported and could be used to explore amphipod evolutionary history at various taxonomic levels (Bauzà-Ribot et al, 2009;Ito et al, 2010;Ki et al, 2010;Kilpert & Podsiadlowski, 2010;Krebes & Bastrop, 2012;Pons et al, 2014;Aunins et al, 2016;Romanova et al, 2016c).…”

Section: Introductionmentioning

confidence: 99%

“…By contrast, the small and circular mt genome is more easily accessible. As a consequence, more than 20 amphipod mt genomes have been sequenced, although many are incomplete (Bauzà-Ribot et al, 2009;Ito et al, 2010;Ki et al, 2010;Kilpert & Podsiadlowski, 2010;Bauzà-Ribot et al, 2012;Krebes & Bastrop, 2012;Shin et al, 2012;Pons et al, 2014;Aunins et al, 2016;Lan et al, 2016;Romanova et al, 2016a, b, c;Stokkan et al, 2016;Macher et al, 2017a).…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome of Gammarus roeselii (Crustacea, Amphipoda): insights into mitogenome plasticity and evolution

et al. 2018