Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
Highlights
Traditional molecular systematic research has been largely dependent on phylogenetic reconstructions based on few molecular markers obtained via individual targeted polymerase chain reaction (PCR) and Sanger sequencing approaches[1,2,3,4,5,6,7]
While these studies provide an early hint on the heterogeneous nature of decapod mitogenomes, reporting novel gene orders in multiple lineages, phylogenetic and comparative genomic studies remained severely constrained by limited taxon sampling for almost a decade[23,24,25,26,27,28]
We provide an overview of the distribution of mitochondrial gene orders (MGO) within the context of our inferred phylogeny and show that these rearrangements are unevenly distributed throughout Decapoda
Summary
Traditional molecular systematic research has been largely dependent on phylogenetic reconstructions based on few molecular markers obtained via individual targeted polymerase chain reaction (PCR) and Sanger sequencing approaches[1,2,3,4,5,6,7]. After the study by Miller and colleagues[24,25], the number of decapod mitogenomes has expanded rapidly ( numbering in the hundreds), proving a valuable resource for studies that have provided new insights into decapod evolutionary relationships and comparative mitogenomics at various taxonomic levels[11,29,30,31,32,33,34,35,36] Despite this progress, sampling within this large and diverse group has generally been skewed towards commercial or -sampled species, highlighting the need for more balanced taxonomic sampling[17,36,37,38]. Similar to insects[62], MGO patterns have been identified as potential synapomorphies for various decapod groups at a range of taxonomic levels, in some instances providing unequivocal resolution of contentious evolutionary relationships[31,32,34,66,67,68,69]
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