Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

Abstract

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina’s HiSeq and MiSeq, Roche’s 454 GS FLX, and Life Technologies’ Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.

Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

“…The latter two models require the input data to be non-partitioned. The CAT-GTR site mixture model implemented in Phylobayes-MPI 1.7a (Lartillot et al, 2007) allows for site-specific rates of mutation, which is considered to be a more realistic model of amino acid evolution, especially for large multi-gene alignments (Maddock et al, 2016). GHOST model is an edge-unlinked mixture model consisting of several site classes with separate sets of model parameters and edge lengths on the same tree topology, thus naturally accounting for heterotachous evolution (Crotty et al, 2017).…”

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

“…The mitogenome enrichment strategy recently proposed by Macher et al (2017b) may be highly relevant in this context. Alternatively, a more affordable strategy may consist in extending sampling in a pilot assay to identify mt genome regions with high information content, which may then be targeted by PCR using primers designed for indexed multiplex amplicon sequencing (Maddock et al, 2016;Meimberg et al, 2016). In our phylogenetic analysis, G. roeselii, G. fossarum and G. pulex form a well-supported clade, a feature also observed in other studies based on either a limited set of partial mt DNA and nuclear DNA sequences (e.g., Hou et al, 2011) or a set of 13 mt protein-coding genes (Macher et al, 2017a).…”

Endemic, endangered and evolutionarily significant: cryptic lineages in Seychelles’ frogs (Anura: Sooglossidae)

“…Recently identified phylogeographic patterns within the archipelago's endemic herpetofauna have revealed a variety of geographic correlations: skinks and geckos broadly differentiate into northern (Praslin and surrounding islands) and southern (Mahé, Silhouette, and surrounding islands) groups (Rocha et al, 2010;Rocha et al, 2011;Valente et al, 2013;Rocha et al, 2016a;Rocha et al, 2016b); while for the nonsooglossid anurans, a distinct lack of variability is shown in the multi-distributed treefrog Tachycnemis seychellensis (Maddock et al, 2014), conflicting with observed structuring in Seychelles endemic caecilians (Adamson et al, 2016;Maddock et al, 2016;Maddock et al, 2017). Our mtDNA analyses appear to confirm the relationship posited by Taylor et al (2012), namely that Silhouette and Praslin populations of So.…”