Nucleotide Composition of CO1 Sequences in Chelicerata (Arthropoda): Detecting New Mitogenomic Rearrangements

Abstract

Here we study the evolution of nucleotide composition in third codon-positions of CO1 sequences of Chelicerata, using a phylogenetic framework, based on 180 taxa and three markers (CO1, 18S, and 28S rRNA; 5,218 nt). The analyses of nucleotide composition were also extended to all CO1 sequences of Chelicerata found in GenBank (1,701 taxa). The results show that most species of Chelicerata have a positive strand bias in CO1, i.e., in favor of C nucleotides, including all Amblypygi, Palpigradi, Ricinulei, Solifugae, Uropygi, and Xiphosura. However, several taxa show a negative strand bias, i.e., in favor of G nucleotides: all Scorpiones, Opisthothelae spiders and several taxa within Acari, Opiliones, Pseudoscorpiones, and Pycnogonida. Several reversals of strand-specific bias can be attributed to either a rearrangement of the control region or an inversion of a fragment containing the CO1 gene. Key taxa for which sequencing of complete mitochondrial genomes will be necessary to determine the origin and nature of mtDNA rearrangements involved in the reversals are identified. Acari, Opiliones, Pseudoscorpiones, and Pycnogonida were found to show a strong variability in nucleotide composition. In addition, both mitochondrial and nuclear genomes have been affected by higher substitution rates in Acari and Pseudoscorpiones. The results therefore indicate that these two orders are more liable to fix mutations of all types, including base substitutions, indels, and genomic rearrangements.

Biodiversity and phylogeny of Ammotheidae (Arthropoda: Pycnogonida)

“…This effect is particularly misleading for Ammotheidae because their diversification is assumed to be ancient, as revealed by their remarkable morphological diversity and by our analyses of 18S and CO1 genes (up to 25% divergence between ammotheid CO1 sequences). In this context, and given that the 18S gene is more appropriate for studying the deepest nodes of arthropod classes (e.g., Arabi et al 2012), we conclude that our nuclear gene gave accurate information for the monophyly of Ammotheidae, Ammotheinae and Achelinae. Morphologically, all representatives of Ammotheidae sensu Bouvier (1923) share the structure of the ovigers with feeble strigilis, without rows of compound spines, and generally without terminal claw.…”

“…in order to limit artefacts during phylogenetic reconstruction. This strategy was determined in agreement with previous studies showing that asymmetric mutational constraints occurred during the evolution of the mitochondrial genome of Chelicerata, including sea spiders Hassanin 2006;Arabi et al , 2012. The 18S alignment was achieved using a first trial with CodonCode Aligner v. 3.7.1, and it was optimized manually on Se-Al v. 2.0a11.…”

“…In contrast, all species of the "Achelia sawayai group" clade have positive AT and CG skews, and those of the Ammotheinae clade generally show a positive CG skew associated with a non-significant AT skew. As pointed out in previous studies, important differences in base composition of mtDNA genes may be misleading for phylogenetic inferences, because they can produce artefacts such as Long Branch Attraction (LBA), when distantly related taxa with similar base composition tend to group together, or the opposite, Long Branch Repulsion (LBR), when closely related taxa with reverse strand-specific biases do not group together Hassanin 2006;Arabi et al , 2012.…”

“…In support of that hypothesis, they showed that two kinds of mitogenomic inversions can lead to a reversal in nucleotide composition: (1) inversion of the control region can result in a global reversal of asymmetric mutational constraints; (2) inversion of a genomic fragment can result in a local reversal of asymmetric mutational constraints. Several reversals of strand specific bias were identified in CO1 sequences of Chelicerata (Arabi et al , 2012 including the common ancestors of Scorpiones and Opisthothelae spiders, as well as several taxa within Acari, Opiliones, Pseudoscorpiones and Pycnogonida. Within Pycnogonida, Arabi et al ( , 2012 have revealed a strong heterogeneity in base composition, particularly among ammotheids, with taxa characterized by positive AT and CG skews (Achelia assimilis), positive CG skew but no significant bias for AT (Ammothea), negative AT and CG skews (e.g., Achelia hispida Hodge, 1864, Ammothella tuberculata and Nymphopsis duodorsospinosa Hilton, 1942) and negative AT skew but no significant bias for CG (Ammothella appendiculata).…”

“…Several reversals of strand specific bias were identified in CO1 sequences of Chelicerata (Arabi et al , 2012 including the common ancestors of Scorpiones and Opisthothelae spiders, as well as several taxa within Acari, Opiliones, Pseudoscorpiones and Pycnogonida. Within Pycnogonida, Arabi et al ( , 2012 have revealed a strong heterogeneity in base composition, particularly among ammotheids, with taxa characterized by positive AT and CG skews (Achelia assimilis), positive CG skew but no significant bias for AT (Ammothea), negative AT and CG skews (e.g., Achelia hispida Hodge, 1864, Ammothella tuberculata and Nymphopsis duodorsospinosa Hilton, 1942) and negative AT skew but no significant bias for CG (Ammothella appendiculata). Our analyses showed that the situation is even more complex with the detection of two additional categories: taxa with no significant strand-bias (e.g., Nymphopsis) and taxa with negative CG skew but no significant bias for AT (e.g., Tanystylum orbiculare Wilson, 1878).…”